Tracking the recruitment and evolution of snake toxins using the evolutionary context provided by the Bothrops jararaca genome.

Venom is a key adaptive innovation in snakes, and how nonvenom genes were co-opted to become part of the toxin arsenal is a significant evolutionary question. While this process has been investigated through the phylogenetic reconstruction of toxin sequences, evidence provided by the genomic context of toxin genes remains less explored. To investigate the process of toxin recruitment, we sequenced the genome of Bothrops jararaca, a clinically relevant pitviper. In addition to producing a road map with canonical structures of genes encoding 12 toxin families, we inferred most of the ancestral genes for their loci. We found evidence that 1) snake venom metalloproteinases (SVMPs) and phospholipases A2 (PLA2) have expanded in genomic proximity to their nonvenomous ancestors; 2) serine proteinases arose by co-opting a local gene that also gave rise to lizard gilatoxins and then expanded; 3) the bradykinin-potentiating peptides originated from a C-type natriuretic peptide gene backbone; and 4) VEGF-F was co-opted from a PGF-like gene and not from VEGF-A. We evaluated two scenarios for the original recruitment of nontoxin genes for snake venom: 1) in locus ancestral gene duplication and 2) in locus ancestral gene direct co-option. The first explains the origins of two important toxins (SVMP and PLA2), while the second explains the emergence of a greater number of venom components. Overall, our results support the idea of a locally assembled venom arsenal in which the most clinically relevant toxin families expanded through posterior gene duplications, regardless of whether they originated by duplication or gene co-option.

The origin and diversification of a novel protein family in venomous snakes.

The genetic origins of novelty are a central interest of evolutionary biology. Most new proteins evolve from preexisting proteins but the evolutionary path from ancestral gene to novel protein is challenging to trace, and therefore the requirements for and order of coding sequence changes, expression changes, or gene duplication are not clear. Snake venoms are important novel traits that are comprised of toxins derived from several distinct protein families, but the genomic and evolutionary origins of most venom components are not understood. Here, we have traced the origin and diversification of one prominent family, the snake venom metalloproteinases (SVMPs) that play key roles in subduing prey in many vipers. Genomic analyses of several rattlesnake (Crotalus) species revealed the SVMP family massively expanded from a single, deeply conserved adam28 disintegrin and metalloproteinase gene, to as many as 31 tandem genes in the Western Diamondback rattlesnake (Crotalus atrox) through a number of single gene and multigene duplication events. Furthermore, we identified a series of stepwise intragenic deletions that occurred at different times in the course of gene family expansion and gave rise to the three major classes of secreted SVMP toxins by sequential removal of a membrane-tethering domain, the cysteine-rich domain, and a disintegrin domain, respectively. Finally, we show that gene deletion has further shaped the SVMP complex within rattlesnakes, creating both fusion genes and substantially reduced gene complexes. These results indicate that gene duplication and intragenic deletion played essential roles in the origin and diversification of these novel biochemical weapons.

Differential evolution and neofunctionalization of snake venom metalloprotease domains.

Snake venom metalloproteases (SVMP) are composed of five domains: signal peptide, propeptide, metalloprotease, disintegrin, and cysteine-rich. Secreted toxins are typically combinatorial variations of the latter three domains. The SVMP-encoding genes of Psammophis mossambicus venom are unique in containing only the signal and propeptide domains. We show that the Psammophis SVMP propeptide evolves rapidly and is subject to a high degree of positive selection. Unlike Psammophis, some species of Echis express both the typical multidomain and the unusual monodomain (propeptide only) SVMP, with the result that a lower level of variation is exerted upon the latter. We showed that most mutations in the multidomain Echis SVMP occurred in the protease domain responsible for proteolytic and hemorrhagic activities. The cysteine-rich and disintegrin-like domains, which are putatively responsible for making the P-III SVMPs more potent than the P-I and P-II forms, accumulate the remaining variation. Thus, the binding sites on the molecule's surface are evolving rapidly whereas the core remains relatively conserved. Bioassays conducted on two post-translationally cleaved novel proline-rich peptides from the P. mossambicus propeptide domain showed them to have been neofunctionalized for specific inhibition of mammalian a7 neuronal nicotinic acetylcholine receptors. We show that the proline rich postsynaptic specific neurotoxic peptides from Azemiops feae are the result of convergent evolution within the precursor region of the C-type natriuretic peptide instead of the SVMP. The results of this study reinforce the value of studying obscure venoms for biodiscovery of novel investigational ligands.

Venomics profiling of Thamnodynastes strigatus unveils matrix metalloproteinases and other novel proteins recruited to the toxin arsenal of rear-fanged snakes.

Rear-fanged and aglyphous snakes are usually considered not dangerous to humans because of their limited capacity of injecting venom. Therefore, only a few studies have been dedicated to characterizing the venom of the largest parcel of snake fauna. Here, we investigated the venom proteome of the rear-fanged snake Thamnodynastes strigatus , in combination with a transcriptomic evaluation of the venom gland. About 60% of all transcripts code for putative venom components. A striking finding is that the most abundant type of transcript (∼47%) and also the major protein type in the venom correspond to a new kind of matrix metalloproteinase (MMP) that is unrelated to the classical snake venom metalloproteinases found in all snake families. These enzymes were recently suggested as possible venom components, and we show here that they are proteolytically active and probably recruited to venom from a MMP-9 ancestor. Other unusual proteins were suggested to be venom components: a protein related to lactadherin and an EGF repeat-containing transcript. Despite these unusual molecules, seven toxin classes commonly found in typical venomous snakes are also present in the venom. These results support the evidence that the arsenals of these snakes are very diverse and harbor new types of biologically important molecules.

Gene tree parsimony of multilocus snake venom protein families reveals species tree conflict as a result of multiple parallel gene loss.

The proliferation of gene data from multiple loci of large multigene families has been greatly facilitated by considerable recent advances in sequence generation. The evolution of such gene families, which often undergo complex histories and different rates of change, combined with increases in sequence data, pose complex problems for traditional phylogenetic analyses, and in particular, those that aim to successfully recover species relationships from gene trees. Here, we implement gene tree parsimony analyses on multicopy gene family data sets of snake venom proteins for two separate groups of taxa, incorporating Bayesian posterior distributions as a rigorous strategy to account for the uncertainty present in gene trees. Gene tree parsimony largely failed to infer species trees congruent with each other or with species phylogenies derived from mitochondrial and single-copy nuclear sequences. Analysis of four toxin gene families from a large expressed sequence tag data set from the viper genus Echis failed to produce a consistent topology, and reanalysis of a previously published gene tree parsimony data set, from the family Elapidae, suggested that species tree topologies were predominantly unsupported. We suggest that gene tree parsimony failure in the family Elapidae is likely the result of unequal and/or incomplete sampling of paralogous genes and demonstrate that multiple parallel gene losses are likely responsible for the significant species tree conflict observed in the genus Echis. These results highlight the potential for gene tree parsimony analyses to be undermined by rapidly evolving multilocus gene families under strong natural selection.

Procoagulant snake toxins: laboratory studies, diagnosis, and understanding snakebite coagulopathy.

Procoagulant toxins are important hemotoxins that have been investigated both as laboratory reagents and potential therapeutic agents. In human envenomation by some elapid and many viperid snakes, these toxins result in venom-induced consumption coagulopathy. Overall, the coagulant activity of the various venoms is difficult to characterize, and many studies simply characterize toxin conversion of isolated substrates, such as the effect of a snake toxin on purified fibrinogen, or on multiple single substrates. As the full effects of toxins on the coagulation pathway are rarely examined, even in vitro, our understanding of the pathophysiology of envenoming is limited. Although prothrombin activators cause a single effect in vitro, there may be complete consumption of fibrinogen, factor V, and factor VIII in vivo due to the downstream effects of the thrombin that is formed. Laboratory diagnosis is a key part of the treatment of snakebite coagulopathy. Assessing which assays are the most informative in snake envenoming, based on the pathophysiology of snakebite coagulopathy, will optimize diagnosis and timing of appropriate coagulation tests. A better understanding of the coagulation effects arising from human envenoming will also improve treatment with antivenom and define the role of adjuvant therapies such as factor replacement.

Peptide fingerprinting of snake venoms by direct infusion nano-electrospray ionization mass spectrometry: potential use in venom identification and taxonomy.

Fingerprinting by mass spectrometry has been increasingly used to study venom variations and for taxonomic analyses based on venom components. Most of these studies have concentrated on components heavier than 3 kDa, but Bothrops snake venoms contain many biologically active peptides, principally C-type natriuretic peptides and bradykinin-potentiating peptides (BPPs). In this work, we have examined the peptide profile of Bothrops venoms (B. alternatus, B. erythromelas, B. insularis, B. jararaca, B. jararacussu, B. leucurus and B. moojeni) using direct infusion nano-electrospray ionization mass spectrometry (nano-ESI-MS) subjecting the data further to principal components analysis (PCA) to assess whether the peptide distributions are reliable in distinguishing the venoms. ESI-MS of a low molar mass fraction obtained by ultrafiltration of each venom (5 kDa nominal cutoff filters) revealed that the venoms have a variety of peptides in common but that each venom also contains taxonomic marker peptides not shared with other venoms. One BPP peptide, QGGWPRPGPEIPP, was found to be common to the seven Bothrops species examined. This peptide may represent a specific marker for this genus since it was not found in the venom of the South American rattlesnake, Crotalus durissus terrificus. PCA on the ESI-MS data reveals a close relationship between B. jararaca, B. jararacussu and B. moojeni venoms, with B. leucurus and B. erythromelas being more distant from these three; B. alternatus and B. insularis were also located distant from these five species, as was C. d. terrificus. These results agree partially with established phylogenetic relationships among these species and suggest that ESI-MS peptide fingerprinting of snake venoms coupled with PCA is a useful tool for identifying venoms and for taxonomic analyses.

[Study on the venoms of the principal venomous snakes from French Guiana and the neutralization]. / Etude des venins des principaux serpents venimeux de Guyane française et de leur neutralisation.

We studied some biochemical, toxic and immunological characteristics of the venoms of Bothrops atrox, Bothrops brazili and Lachesis muta, Viperidae responsible for most of the bites of venomous snakes in French Guiana. Chromatographic (HPLC) and electrophoretical profiles (SDS-PAGE), lethal, hemorrhagic, defibrinogenating, coagulant, thrombin like, proteolytic, fibrino(geno)lytic and phospholipase activities were studied. In addition, the neutralization of some toxic activities conferred by four antivenins was compared. The chromatographic and electrophoretic profiles were different for the three venoms, showing differences between Bothrops and L. muta venoms. In general, bothropic venoms showed the highest toxic and enzymatic activities, while the venom of L. muta showed the lowest lethal, hemorrhagic and coagulant activities. The enzymes of bothropic venoms responsible for gelatinolytic activity were around 50-90 kDa. All the venoms were able to hydrolyze a and beta chains of the fibrinogen, showing different patterns of degradation. Although all the antivenoms tested were effective to various degrees in neutralizing the venom of B. brazili and B. atrox, neutralization of L. muta venom was significantly better achieved using the antivenom including this venom in its immunogenic mixture. For the neutralization of L. muta venom, homologous or polyvalent antivenoms that include the "bushmaster" venom in their immunogenic mixture should be preferred.

DNA barcodes from snake venom: a broadly applicable method for extraction of DNA from snake venoms.

DNA barcoding is a simple technique used to develop a large-scale system of classification that is broadly applicable across a wide variety of taxa. DNA-based analysis of snake venoms can provide a system of classification independent of currently accepted taxonomic relationships by generating DNA barcodes specific to each venom sample. DNA purification from dried snake venoms has previously required large amounts of starting material, has resulted in low yields and inconsistent amplification, and was possible with front-fanged snakes only. Here, we present a modified DNA extraction protocol applied to venoms of both front- and rear-fanged snakes that requires significantly less starting material (1 mg) and yields sufficient amounts of DNA for successful PCR amplification of regions commonly used for DNA barcoding. [Formula: see text].

Some aspects of the venom proteome of the Colubridae snake Philodryas olfersii revealed from a Duvernoy's (venom) gland transcriptome.

We investigated the putative toxins of Philodryas olfersii (Colubridae), a representative of a family of snakes neglected in venom studies despite their growing medical importance. Transcriptomic data of the venom gland complemented by proteomic analysis of the gland secretion revealed the presence of major toxin classes from the Viperidae family, including serine proteases, metalloproteases, C-type lectins, Crisps, and a C-type natriuretic peptide (CNP). Interestingly, the phylogenetic analysis of the CNP precursor showed it as a linker between two related precursors found in Viperidae and Elapidae snakes. We suggest that these precursors constitute a monophyletic group derived from the vertebrate CNPs.

Molecular barcoding, DNA from snake venom, and toxinological research: Considerations and concerns.

The problem of species identification in toxinological research and solutions such as molecular barcoding and DNA extraction from venom samples are addressed. Molecular barcoding is controversial with both perceived advantages and inherent problems. A method of species identification utilizing mitochondrial DNA from venom has been identified. This method could result in deemphasizing the importance of obtaining detailed information on the venom source prior to analysis. Additional concerns include; a cost prohibitive factor, intraspecific venom variation, and venom processing issues. As researchers demand more stringent records and verification, venom suppliers may be prompted to implement improved methods and controls.

Snake venoms and their toxins: an Australian perspective.

Australia is home to a vast collection of highly venomous terrestrial and marine snakes. As such, Australia has proven to be an excellent source of investigative material for both local and international toxinologists. Research on snake venoms initially focussed on identifying the most lethal species, and the venom components responsible for the lethality, so that treatment strategies could be implemented. Since then, the focus of research has included the isolation and characterisation of toxins (primarily neurotoxins), examination of the efficacy of commercially available antivenoms and, more recently, the use of liquid chromatography/mass spectrometry (LCMS) to aid in the analysis of whole venoms. Given the vast quantity of research undertaken over the past 70 yr we have tried to provide a short insight into some of this excellent work and identify areas requiring further examination.

[The problem of intoxication in the population of the Republic of Guinea due to venomous snake bites].

Intoxication of the population of Guinea due to venomous snake bites (100-150 intoxications per 100,000 with an 18% mortality rate) is a serious public health problem in the Republic of Guinea. Guinea's fauna of venomous snakes is diverse and numbers 20 species that are dangerous to human beings. The representatives of the family Elapidae (cobras and mambas) whose venom is highly toxic (LD50 5-12 mg) are responsible for the bulk (59.6%) of their bites. There has been recently an increase in the number of deaths from venomous snake bites, as high as 60% of the patients consulting a doctor being notified in one of the prefectures. At the same time the situation associated with the availability of antisnake serum is critical in the country due to its minute amount and to the inaccessibility of its high prices. By taking into account the great demand for the serum in Guinea, as everywhere over West Africa (thousands of doses every year), its manufacture may be profitable for potential investors and partners of the Pasteur Institute of Guinea.

Categorization of venoms according to bonding properties: An immunological overview.

In this report, we present a study on the antigenic cross-reactivity of various venoms from the most dangerous Egyptian snakes and scorpions belonging to families Elapidae, Viperidae and Buthidae. The study was carried out with special reference to bonding properties between venoms and antivenoms and their involvement in the formation of specific and/or cross-reactive interactions. The homologous polyclonal antivenoms showed high reactivity to the respective venoms and cross-reacted with varying degrees to other non-homologous venoms. Assorting the antivenoms according to their susceptibility to dissociation by different concentrations of NH4SCN revealed that most of the antibodies involved in homologous venom-antivenom interactions were highly avid; building up strong venom-antivenom bonding. Whereas cross-reactions due to heterologous interactions were mediated by less avid antibodies that ultimately led to the formation of venom-antivenom bonding of different power strengths depending on the antigenic similarity and hence on the phylogenetic relationship of the tested venom. A new parameter evaluating high and low avid interactions, designated as H/L value, for each antigen-antibody bonding was initiated and used as an indicator of bonding strength between different venom-antivenom partners. H/L values were many folds higher than 1 for homologous and closely related venoms, 1 or around 1 for cross-reactive venoms, whereas venoms from unrelated remote sources recorded H/L values far less than 1. Using well defined polyclonal antivenoms, H/L value was successfully used to assign eight unknown venoms to their animal families and the results were confirmed by species-specific ELISA and immunoblotting assays.

Development of Equine IgG Antivenoms against Major Snake Groups in Mozambique.

BACKGROUND: Snake envenoming is a significant public health problem in underdeveloped and developing countries. In sub-Saharan Africa, it is estimated that 90,000-400,000 envenomations occur each year, resulting in 3,500-32,000 deaths. Envenomings are caused by snakes from the Viperidae (Bitis spp. and Echis spp.) and Elapidae (Naja spp. and Dendroaspis spp.) families. The African continent has been suffering from a severe antivenom crisis and current antivenom production is only sufficient to treat 25% of snakebite cases. Our aim is to develop high-quality antivenoms against the main snake species found in Mozambique. METHODS: Adult horses primed with the indicated venoms were divided into 5 groups (B. arietans; B. nasicornis + B. rhinoceros; N. melanoleuca; N. mossambica; N. annulifera + D. polylepis + D. angusticeps) and reimmunized two times for antivenom production. Blood was collected, and plasma was separated and subjected to antibody purification using caprylic acid. Plasmas and antivenoms were subject to titration, affinity determination, cross-recognition assays and in vivo venom lethality neutralization. A commercial anti-Crotalic antivenom was used for comparison. RESULTS: The purified antivenoms exhibited high titers against B. arietans, B. nasicornis and B. rhinoceros (5.18 x 106, 3.60 x 106 and 3.50 x 106 U-E/mL, respectively) and N. melanoleuca, N. mossambica and N. annulifera (7.41 x 106, 3.07 x 106 and 2.60 x 106 U-E/mL, respectively), but lower titers against the D. angusticeps and D. polylepis (1.87 x 106 and 1.67 x 106 U-E/mL). All the groups, except anti-N. melanoleuca, showed significant differences from the anti-Crotalic antivenom (7.55 x 106 U-E/mL). The affinity index of all the groups was high, ranging from 31% to 45%. Cross-recognition assays showed the recognition of proteins with similar molecular weight in the venoms and may indicate the possibility of paraspecific neutralization. The three monospecific antivenoms were able to provide in vivo protection. CONCLUSION: Our results indicate that the anti-Bitis and anti-Naja antivenoms developed would be useful for treating snakebite envenomations in Mozambique, although their effectiveness should to be increased. We propose instead the development of monospecific antivenoms, which would serve as the basis for two polyvalent antivenoms, the anti-Bitis and anti-Elapidae. Polyvalent antivenoms represent an increase in treatment quality, as they have a wider range of application and are easier to distribute and administer to snake envenoming victims.

Estimates of disease burden due to land-snake bite in Sri Lankan hospitals.

Snake bite is a common cause of hospital admission in Sri Lanka. Despite this, there have been no countrywide studies or national estimates of disease burden due to snake bites in Sri Lankan hospitals. We assessed the disease burden due to snake bite in our hospitals and estimated the frequency of admissions due to bites by different snake species. Sri Lanka was divided into four zones based on climate and topography. Hospital morbidity and mortality data, which are available on an administrative district basis, were collated for the four zones. A survey of opinion among specialist physicians (the Delphi technique) was used to estimate the proportion of bites by different species, and requirements for anti-venom (AV) and intensive care facilities for management of snake bites in hospitals in each of the four zones. A study of hospital admissions due to snake bites in seven selected hospitals was also performed to validate the opinion survey. There was a clear difference in the incidence of hospital admissions due to snake bites in the different zones. Estimates of hospital admissions due to bites by different species also varied considerably between zones. These trends corresponded to estimates of requirements of AV and other supportive health care. Health care planning using data based on environmental information, rather than merely on political boundaries, could lead to targeted distribution of AV and intensive care requirements to manage snake bites.

Venom gland transcriptomics for identifying, cataloging, and characterizing venom proteins in snakes.

Snake venoms are cocktails of protein toxins that play important roles in capture and digestion of prey. Significant qualitative and quantitative variation in snake venom composition has been observed among and within species. Understanding these variations in protein components is instrumental in interpreting clinical symptoms during human envenomation and in searching for novel venom proteins with potential therapeutic applications. In the last decade, transcriptomic analyses of venom glands have helped in understanding the composition of various snake venoms in great detail. Here we review transcriptomic analysis as a powerful tool for understanding venom profile, variation and evolution.

Astacins, serralysins, snake venom and matrix metalloproteinases exhibit identical zinc-binding environments (HEXXHXXGXXH and Met-turn) and topologies and should be grouped into a common family, the 'metzincins'.

The X-ray crystal structures of two zinc endopeptidases, astacin from crayfish, and adamalysin II from snake venom, reveal a strong overall topological equivalence and virtually identical extended HEXXHXXGXXH zinc-binding segments, but in addition a methionine-containing turn of similar conformation (the 'Met-turn'), which forms a hydrophobic basis for the zinc ion and the three liganding histidine residues. These two features are also present in a similar arrangement in the matrix metalloproteinases (matrixins) and in the large bacterial Serratia proteinase-like peptidases (serralysins). We suggest that these four proteinases represent members of distinct subfamilies which can be grouped together in a family, for which we propose the designation, metzincins.

Synopsis of recent developments in venomous snake systematics, No. 3.

We present recent findings in the systematics of venomous snakes, with emphasis on those which affect the nomenclature and our understanding of species limits in these animals. Changes in systematics reviewed here include particularly the genera Acanthophis, Elapsoidea, Bitis, Lachesis, Porthidium, Trimeresurus/Tropidolaemus and Vipera. Other new publications of more general interest to toxinologists are also presented.

Pharmacological modulation of edema induced by Lys-49 and Asp-49 myotoxic phospholipases A2 isolated from the venom of the snake Bothrops asper (terciopelo).

The pharmacological modulation of edema-forming activity of Bothrops asper myotoxins II and III, Lys-49 and Asp-49 phospholipases A2, respectively, was studied plethysmographically in the mouse foot pad model. Myotoxin III had phospholipase A2 activity, whereas myotoxin II was devoid of enzymatic activity when tested on egg yolk phosphatidylcholine. Both toxins induced a dose-dependent edema of rapid onset. Chemical modification of myotoxin III with p-bromophenacyl bromide abrogated enzymatic activity and significantly reduced edemat-forming activity, although a residual effect remained. Pre-treatment of animals with diphenhydramine, dexamethasone, indomethacin and prazosin significantly reduced the effect of both myotoxins. It is concluded that (a) these myotoxins are important edema-forming components of B. asper venom, (b) enzymatic activity is not a strict requirement to exert this effect, although in the case of myotoxin III it contributes to its development, and (c) several inflammatory mediators participate in mouse foot pad edema induced by these myotoxins.