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34 results for “venomous snake”
Dataset from "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2‑like Peptides"
<p>Dataset from "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2‑like Peptides", containing the most relevant all-atom output trajectories and input files ran with GROMACS 2021:</p> <p>1) <strong>pure_membrane_systems.7z</strong> - pure bilayer systems (AA1, AA2, AA5), including equilibration, calcium insertion, and umbrella sampling simulations;</p> <p>2) <strong>single_peptide_systems.7z</strong> - single peptide-containing systems (AA3, AA4, AA6), including equilibration, calcium insertion, and umbrella sampling simulations;</p> <p>3) <strong>multiple_peptide_systems.7z</strong> - multiple peptide-containing systems (AA7, AA8), including equilibration, calcium insertion, and umbrella sampling simulations.</p> <p>We have included the input files (.mdp), system topology (.top and .itp), initial and final structure files (.gro), the index file (.ndx), and the portable binary run input files (.tpr). We have also included the output trajectories of systems AA3, AA4, AA6-8 in .xtc format, and spaced every 500 ps.</p> <p>System composition is given in Table Z1. More details can be found in the related publication.</p> <p><strong>Table Z1. Simulated systems' details, including name, composition (in number of lipid and peptide molecules), number of atoms composing the systems, simulation (sim.) time, and total umbrella sampling (US) time.</strong> </p> <table> <tbody> <tr> <td><strong>System</strong></td> <td><strong>POPC/POPS/Peptide</strong></td> <td><strong>no. atoms (a)</strong></td> <td><strong>sim. time (µs)</strong></td> <td><strong>US time (µs)</strong></td> </tr> <tr> <td><strong>AA1</strong></td> <td>128/0/0</td> <td>40,226</td> <td>0.3</td> <td>10.8</td> </tr> <tr> <td><strong>AA2</strong></td> <td>0/128/0</td> <td>39,458</td> <td>0.3</td> <td>10.8</td> </tr> <tr> <td><strong>AA3</strong></td> <td>128/0/1</td> <td>40,504</td> <td>0.5</td> <td>32.3</td> </tr> <tr> <td><strong>AA4</strong></td> <td>0/128/1</td> <td>39,724</td> <td>0.5</td> <td>32.3</td> </tr> <tr> <td><strong>AA5</strong></td> <td>96/32/0</td> <td>40,034</td> <td>1.0</td> <td>-</td> </tr> <tr> <td><strong>AA6</strong></td> <td>96/32/1</td> <td>40,300</td> <td>1.0</td> <td>-</td> </tr> <tr> <td><strong>AA7</strong></td> <td>96/32/5</td> <td>41,364</td> <td>1.0</td> <td>10.8</td> </tr> <tr> <td><strong>AA8</strong></td> <td>96/32/13</td> <td>55,128</td> <td>2.0</td> <td>10.8</td> </tr> </tbody> </table> <p>(a) for the US simulations, the total number of atoms was reduced in 1 because two sodium ions were substituted by a single calcium ion.</p>
DATASET - Mass Spectrometry - Snake venom proteomics of three subspecies of the North African mountain viper (Vipera monticola, Saint-Girons 1954) from Morocco
<p><strong>This DATASET collection includes the mass spectrometry files for proteomics venom investigation of three subspecies of the North African mountain viper (<em>Vipera monticola</em>, Saint-Girons 1954) from Morocco.</strong></p> <p><strong>Species list:</strong></p> <ol> <li>Vipera monticola monticola</li> <li>Vipera monticola atlantica</li> <li>Vipera monticola saintgironsi</li> </ol> <p><strong>Folders 01-03 - BOTTOM-UP PROTEOMICS</strong>: The venom pools were investigated by the bottom-up "snake venomics" (labled as SVX) approach and in short: separated by RP-HPLC, followed by SDS-PAGE separation and the single bands were in-gel processed by DTT, IAC and finally o/n tryptic digested. Samples submitted to HPLC-MS/MS. Early peptidic fractions of the first HPLC run were directly submitted to HPLC-MS/MS analytic w/o further gel procession. Folders 01 to 03 include the MS and MS/MS spectra of the snake species 1-3, respectively. Files are included as RAW and MZML format.</p> <p>Used instrument: LTQ Orbitrap XL mass spectrometer (Thermo, Bremen, Germany) with an Agilent 1260 HPLC system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Grace Vydac 218MS C18 (2.1 × 150 mm; 5 μm particle size) column.</p> <p>Modifications: UNIMOD:4 - \"Iodoacetamide derivative.\"</p> <p>Used protein database: Uniprot_8570_serpentes_reviewed_CandIso_2747_entries_230398.fasta</p>
DATASET - Mass Spectrometry - Snake venom proteomics of island and mainland V. ammodytes populations from North Macedonia
<p><strong><span>This DATASET collection includes the mass spectrometry files for proteomics venom investigation of island and mainland <em>V. ammodytes</em> populations from North Macedonia.</span></strong></p> <p><strong><span>Sample list:</span></strong></p> <ol> <li><span>Island - adult - male</span></li> <li><span>Island - adult - female</span></li> <li><span>Island - juvenile</span></li> <li><span>Island - subadult</span></li> <li><span>Mainland - adult</span></li> <li><span>Mainland - subadult</span></li> <li><span>Mainland - juvenile</span></li> </ol> <p><strong><span>Folders 01-07 - BOTTOM-UP PROTEOMICS</span></strong><span>: The venom pools were investigated by the bottom-up "snake venomics" (labelled as SVX) approach and in short: separated by RP-HPLC, followed by SDS-PAGE separation and the single bands were in-gel processed by DTT, IAC and finally o/n tryptic digested. Samples submitted to HPLC-MS/MS. Early peptidic fractions of the first HPLC run were directly submitted to HPLC-MS/MS analytic w/o further gel procession. Folders 01 to 07 include the MS and MS/MS spectra of the <em>V. ammodytes</em> sample pools from different populations. Files are included as RAW and MZML format.</span></p> <p><span>Used instrument: LTQ Orbitrap XL mass spectrometer (Thermo, Bremen, Germany) with an Agilent 1260 HPLC system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Grace Vydac 218MS C18 (2.1 × 150 mm; 5 </span><span>μ</span><span>m particle size) column.</span></p> <p><span>Modifications: UNIMOD:4 - \"Iodoacetamide derivative.\"</span></p> <p><span>Used protein database: Uniprot_8750_serpentes_CanNIso_2674_entries_220210_cRAP_220210.fasta</span></p>
Figure 7 in The evolution of venom-delivery systems in snakes
Figure 7. Most parsimonious reconstructions of the evolution of fang character states, with characters ordered, in the context of the phylogenies of (A) Cadle (1988) and (B) Kraus & Brown (1998). The Kraus & Brown tree is an example of just one of seven equally parsimonious reconstructions. U, ungrooved; G, grooved; and T, tubular.
Figure 6 in The evolution of venom-delivery systems in snakes
Figure 6. Most parsimonious recontruction of the evolution of the position of attachment of the pterygoideus within the context of the hypotheses of (A) Cadle (1988) and (B) Kraus & Brown (1998). A, anterior attachment near the posterior maxillary teeth, on the posterior end of the maxilla; P, anterior attachment on the ectopterygoid (i.e. posterior).
Figure 4 in The evolution of venom-delivery systems in snakes
Figure 4. Most parsimonious reconstruction of the evolution of venom glands and Duvernoy's glands in the context of (A) Cadle's (1988) and (B) Kraus & Brown's (1998) phylogeny. X, Duvernoy's gland and venom gland absent; D, Duvernoy's gland present; VV, venom gland of viperid type present; VE, venom gland of elapid type present; VA, venom gland of atractaspidid type present.
Data on global expression of non-coding RNome in mice gastrocnemius muscle exposed to jararhagin, snake venom metalloproteinase
<p>This study describes the data on the global expression profile of small RNA (smRNAs) molecules in mice gastrocnemius muscle exposed to jararhagin, snake venom metalloproteinase. The data include smRNAs and microRNAs in mice gastrocnemius muscle challenged with Jararhagin (Jar; n=4) in the right paw or phosphate-buffered saline (PBS; control; n=4) in the left paw. smRNA-Seq libraries were generated after 24hs of exposure to PBS or jararhagin. </p>
DATASET - Mass Spectrometry - Snake venom proteomics of seven taxa of the genera Vipera, Montivipera, Macrovipera and Daboia across Türkiye
<p><strong>Publication: Damm <em>et al.</em> 2024 - <a title="DOI URL" href="https://doi.org/10.1021/acs.jproteome.4c00171">https://doi.org/10.1021/acs.jproteome.4c00171</a></strong></p> <p> </p> <p><strong>This DATASET collection includes the mass spectrometry files for proteomics venom investigation of seven taxa of the genera <em>Vipera</em>, <em>Montivipera</em>, <em>Macrovipera</em> and <em>Daboia </em>across Türkiye.</strong></p> <p><strong>Species list:</strong></p> <ol> <li>Vipera berus barani</li> <li>Vipera darevskii</li> <li>Montivipera bulgardaghica bulgardaghica </li> <li>Montivipera bulgardaghica albizona</li> <li>Montivipera xanthina</li> <li>Macrovipera lebetinus obtusa</li> <li>Daboia palaestinae</li> </ol> <p><strong>Folders 01-07 - BOTTOM-UP PROTEOMICS</strong>: The venom pools were investigated by the bottom-up "snake venomics" (labled as SVX) approach and in short: separated by RP-HPLC, followed by SDS-PAGE separation and the single bands were in-gel processed by DTT, IAC and finally o/n tryptic digested. Samples submitted to HPLC-MS/MS. Early peptidic fractions of the first HPLC run were directly submitted to HPLC-MS/MS analytic w/o further gel procession. Folders 01 to 07 include the MS and MS/MS spectra of the snake species 1-7, respectively. Files are included as RAW and MZML format.</p> <p>Used instrument: LTQ Orbitrap XL mass spectrometer (Thermo, Bremen, Germany) with an Agilent 1260 HPLC system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Grace Vydac 218MS C18 (2.1 × 150 mm; 5 μm particle size) column.</p> <p>Modifications: UNIMOD:4 - \"Iodoacetamide derivative.\"</p> <p>Used protein database: Uniprot_8570_serpentes_reviewed_canonical_2640_entries_cRAP_210408.fasta</p> <p><strong>Folders 10-11 - TOP-DOWN PROTEOMICS</strong>: The venom pools were investigated by the non-reduced and TCEP reduced top-down (labled as TD) approach and in short: untreated or TCEP reduced samples submitted to HPLC-MS/MS. Folders 10 and 11 include the MS and MS/MS spectra of the snake species 1-7 as labled. Files are included as RAW and MZML format.</p> <p>Used instrument: Q Exactive HF mass spectrometer (Thermo, Bremen, Germany) with a Vanquish ultra-high performance liquid chromatography (UHPLC) system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Supelco Discovery BIO wide C18 (2.0 × 150 mm; 3 μm particle size; 300 Å pore size).</p> <p>Modifications: none (either red. or non-red. disulfide bridges)</p> <p>Used protein database for TopPIC analysis: Uniprot_8570_serpentes_reviewed_ISOandCAN_2749_entries_NOcRAP_231011.fasta</p> <p> </p>
DATASET - Mass Spectrometry - Snake venom proteomics of Deinagkistrodon acutus
<p><strong>This DATASET collection includes the mass spectrometry files for shotgun proteomics venom investigation the sharp-nosed viper (<em>Deinagkistrodon acutus</em>) from China.</strong></p> <p><strong>Species list:</strong></p> <ol> <li>Deinagkistrodon acutus</li> </ol> <p><strong>Folders 01-02 - BOTTOM-UP SHOTGUN PROTEOMICS</strong>: The venom pool was investigated by the bottom-up shotgun (labled as SG) approach and in short: in-solution processed by DTT, IAC and finally o/n tryptic digested. Samples submitted to HPLC-MS/MS. Folders includes the MS and MS/MS spectra of Deinagkistrodon acutus. Files are included as RAW and MZML format in folder 01 and 02, respectively.</p> <p>Used instrument:</p> <p>Advion TriVersa NanoMate (Advion BioSciences) into an Orbitrap Eclipse Tribrid MS instrument (Thermo Fisher Scientific) with an UltiMate 3000RSLCnano system (Thermo Fisher Scientific) using 50 cm μPAC C18 column (Pharma Fluidics).</p> <p>Modifications: UNIMOD:4 - \"Iodoacetamide derivative.\"</p>
Figure 2 in The evolution of venom-delivery systems in snakes
Figure 2. Relationships among colubroid snakes proposed by Cadle (1988).
Figure 3 in The evolution of venom-delivery systems in snakes
Figure 3. Relationships among colubroid snakes proposed by Kraus & Brown (1998).
Figure 1 in The evolution of venom-delivery systems in snakes
Figure 1. Phylogenetic relationships among living snakes (Pough et al., 2001).
Snakes on a plain: Complex biotic and abiotic factors determine venom variation in North America's widest-ranging rattlesnake
<p><strong>Background</strong>. Snake venoms are trophic adaptations that represent an ideal model to examine the evolutionary factors that shape polymorphic traits under strong natural selection. Venom compositional variation is substantial within and among venomous snake species. However, the forces shaping this phenotypic complexity, as well as the potential integrated roles of biotic and abiotic factors, have received little attention. Here, we investigate geographic variation in venom composition in a wide-ranging rattlesnake (<em>Crotalus viridis viridis</em>) and contextualize this variation by investigating dietary, phylogenetic, and environmental variables that covary with venom.</p> <p><strong>Results</strong>. Using shotgun proteomics, venom biochemical profiling, and lethality assays, we identify 2 distinct divergent phenotypes that characterize major axes of venom variation in this species: a myotoxin-rich phenotype and a snake venom metalloprotease (SVMP)-rich phenotype. We find that dietary availability and temperature-related abiotic factors are correlated with geographic trends in venom composition.</p> <p><strong>Conclusions</strong>. Our findings highlight the potential for snake venoms to vary extensively within species, for this variation to be driven by biotic and abiotic factors, and for the importance of integrating biotic and abiotic variation for understanding complex trait evolution. Links between venom variation and variation in biotic and abiotic factors indicate that venom variation likely results from substantial geographic variation in selection regimes that determine the efficacy of venom phenotypes across populations and snake species. Our results highlight the <a>implicit </a>influence of abiotic factors on biotic factors that ultimately shape venom phenotype, providing evidence for a central role of local selection as a key driver of venom variation.</p>
Snakes on a plain: Complex biotic and abiotic factors determine venom variation in North America's widest-ranging rattlesnake
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Data from: Diversification rates and phenotypic evolution in venomous snakes (Elapidae)
The relationship between rates of diversification and of body size change (a common proxy for phenotypic evolution) was investigated across Elapidae, the largest radiation of highly venomous snakes. Time-calibrated phylogenetic trees for 175 species of elapids (more than 50% of known taxa) were constructed using seven mitochondrial and nuclear genes. Analyses using these trees revealed no evidence for a link between speciation rates and changes in body size. Two clades (Hydrophis, Micrurus) show anomalously high rates of diversification within Elapidae, yet exhibit rates of body size evolution almost identical to the general elapid 'background' rate. Although correlations between speciation rates and rates of body size change exist in certain groups (e.g. ray-finned fishes, passerine birds), the two processes appear to be uncoupled in elapid snakes. There is also no detectable shift in diversification dynamics associated with the colonization of Australasia, which is surprising given that elapids appear to be the first clade of venomous snakes to reach the continent.
Data from: Medically important differences in snake venom composition are dictated by distinct postgenomic mechanisms
Variation in venom composition is a ubiquitous phenomenon in snakes and occurs both interspecifically and intraspecifically. Venom variation can have severe outcomes for snakebite victims by rendering the specific antibodies found in antivenoms ineffective against heterologous toxins found in different venoms. The rapid evolutionary expansion of different toxin-encoding gene families in different snake lineages is widely perceived as the main cause of venom variation. However, this view is simplistic and disregards the understudied influence that processes acting on gene transcription and translation may have on the production of the venom proteome. Here, we assess the venom composition of six related viperid snakes and compare interspecific changes in the number of toxin genes, their transcription in the venom gland, and their translation into proteins secreted in venom. Our results reveal that multiple levels of regulation are responsible for generating variation in venom composition between related snake species. We demonstrate that differential levels of toxin transcription, translation, and their posttranslational modification have a substantial impact upon the resulting venom protein mixture. Notably, these processes act to varying extents on different toxin paralogs found in different snakes and are therefore likely to be as important as ancestral gene duplication events for generating compositionally distinct venom proteomes. Our results suggest that these processes may also contribute to altering the toxicity of snake venoms, and we demonstrate how this variability can undermine the treatment of a neglected tropical disease, snakebite.
Data from: Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly
Background: While many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ well-integrated systems of proteins and organic constituents to immobilize prey. Venoms are generally optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown. Results: Using next-generation transcriptome sequencing and mass spectrometry, we examined microevolution in two pitvipers, allopatrically separated for at least 1.6 million years, and their hybrids. Transcriptomes of parental species had generally similar compositions in regard to protein families, but for a given protein family, the homologs present and concentrations thereof sometimes differed dramatically. For instance, a phospholipase A 2 transcript comprising 73.4 % of the Protobothrops elegans transcriptome, was barely present in the P. flavoviridis transcriptome (<0.05 %). Hybrids produced most proteins found in both parental venoms. Protein evolutionary rates were positively correlated with transcriptomic and proteomic abundances, and the most abundant proteins showed positive selection. This pattern holds with the addition of four other published crotaline transcriptomes, from two more genera, and also for the recently published king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at Protobothrops, we show that rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptation. Conclusions: Given log-scale differences in toxin abundance, which are likely correlated with biosynthetic costs, we hypothesize that as a result of natural selection, snakes optimize return on energetic investment by producing more of venom proteins that increase their fitness. Natural selection then acts on the additive genetic variance of these components, in proportion to their contributions to overall fitness. Adaptive evolution of venoms may occur most rapidly through changes in expression levels that alter fitness contributions, and thus the strength of selection acting on specific secretome components.
Venom toxins of the annulated sea snake (Hydrophis cyanocinctus)
<p>Table S1. Amino acid sequences translated from toxin unigenes in the venom-gland transcriptome of the annulated sea snake (Hydrophis cyanocinctus) from the South China Sea. Sequences with partial CDS are indicated in italic; Table S2. FPKM% of protein family in the venom-gland transcriptome of the annulated sea snake (Hydrophis cyanocinctus) from the South China Sea; Table S3. Sequences used for positive selection detecting by codeml test; Table S4. Sequences used for positive selection detecting by yn00 test.</p>
Ecological and biogeographic processes drive the proteome evolution of snake venom
<p class="Body"><span>The emergence of venom is an evolutionary innovation that favored the diversification and survival of snakes. The composition of snake venoms is known in detail from venom gland proteomic data. However, there is still a gap of knowledge about the forces that lead to the expression of different toxins in different proportions in the venom cocktail across space and time.</span></p> <p class="Body"><span><b>LOCATION</b></span></p> <p class="Body"><span>World.</span></p> <p class="Body"><span><b>TIME PERIOD</b></span></p> <p class="Body"><span>Modern.</span></p> <p class="Body"><span><b>MAJOR TAXA STUDIED</b></span></p> <p class="Body"><span>Elapidae and Viperidae.</span></p> <p class="Body"><span>We integrated proteomic data with phylogenetic comparative methods to understand how ecological and biogeographical processes drive the evolution of snake venom. </span><span>We observed that more productive environments favor a more complex venom, which presents a higher diversity and similarity on the toxin proportions in its composition. We found that the taxa that live in islands, where there is lower variability of resources, tended to present less complex venom dominated by few toxins. In this case, the island's isolation seems to be a relevant element for a faster fixation of specific venom compositions. </span>We show that ecological and biogeographic processes, which can act differentially over time and space, affect the gene expression of toxins in snake venoms.</p>
Genome-wide SNPs reveal recurrent waves of speciation in niche-pockets, in Europe's most venomous snake
<p>Within the Balkan Peninsula, topographic and climatic agents have promoted biodiversity and shaped the speciation history of many ectotherms. Here, we targeted an iconic European reptile, the nose-horned viper species-complex (<em>Vipera</em> <em>ammodytes</em>), and explored its spatial and temporal evolution. We (1) utilized genome-wide SNPs to infer genetic structure and build a time-calibrated species tree, and (2) applied species distribution modeling (SDM) with niche-divergence tests among major phylogenomic clades. Geographically structured genetic diversity was found. Cycles of recurrent isolation and expansion during glacial–interglacial periods led to allopatric speciation and to secondary contacts and formation of multiple hybrid zones throughout the Balkan Peninsula. Deep divergence is still detected among populations separated by old and imminent biogeographical barriers (e.g. Pindos Mountain Range, the Cyclades islands, etc.), but in most cases, speciation is incomplete. At the other end of the speciation continuum, we recognize two well-differentiated lineages, currently lacking any evidence of gene flow; one is distributed in the Northwestern Balkans and the other in the Southeastern Balkans, further expanding into Asia. Despite their split 5 Mya, there is no evidence of ecological divergence, as speciation probably occurred in niche-pockets of analogous environments. These two lineages probably represent different species, while <em>V. transcaucasiana</em> does not merit species status. By comparing the genomic phylogenies to an updated mitochondrial one, we propose an evolutionary scenario that resolves all mito-nuclear conflicts, according to which the history of the <em>V. ammodytes</em> species-complex was shaped by complex processes, including a major event of introgressive hybridization with asymmetric mitochondrial capture.</p>
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