Multiomics Profiling of Toxins in the Venom of the Amazonian Spider Acanthoscurria juruenicola

Gondwanan relic or recent arrival? The biogeographic origins and systematics of Australian tarantulas

The composition of Australia's fauna and flora has been largely assembled by two biogeographic processes, vicariance and long-distance dispersal and establishment. These patterns can be observed today through the survival of Gondwanan lineages contrasted with relatively recent colonization from south-east Asia, respectively. In general, the post-Gondwanan immigrant lineages from south-east Asia are taxa with traits that facilitate dispersal. Consequently, taxa like tarantulas (Araneae, Theraphosidae) that are largely pan-tropical but also have a low propensity for dispersal, are thought to be Gondwanan in origin. However, the Australian tarantulas are unsampled for phylogenomic studies and, as such, their classification and biogeographic origins have been long debated and are unresolved. Here we test if their current, morphology-based classification in Selenocosmiinae is accurate and assess whether the Australian tarantulas were present in Australia while it was part of Gondwana. We sample 369 tarantula specimens from across Australia, greatly expanding the geographic sampling of previous studies, to develop the first continent-wide phylogeny of the Australian tarantulas. To resolve the 'back bone' of the Australian tarantula phylogeny we generate 20 new transcriptomes for species of Australian tarantulas representing distinct lineages uncovered using mitochondrial sequence data and combine these new transcriptomes with published transcriptomic data. Through the recovery of ultra-conserved element (UCE) loci from transcriptomes and testing multiple data occupancy matrices, we find that the Australian clade is monophyletic and nested inside the largely Asian Selenocosmiinae. We find the Australian fauna are a relatively young radiation with a crown age of 18.8-8.3 Ma and we therefore reject the hypothesis of a Gondwanan origin for these animals and, instead, infer a recent dispersal from south-east Asia. Our findings indicate that they underwent a rapid radiation, possibly coinciding with their arrival into Australia. Our findings refute the monophyly of Selenocosmia and Coremiocnemis as currently recognised, and we remove Selenocosmia stalkeri from synonymy with Selenocosmia stirlingi.

Enhancing the Bothropic Antivenom through a Reverse Antivenomics Approach

Antivenoms are the only effective treatment for snakebite envenomation and have saved countless lives over more than a century. Despite their value, antivenoms present risks of adverse reactions. Current formulations contain a fraction of nonspecific antibodies and serum proteins. While new promising candidates emerge as the next generation of antivenoms, it remains clear that animal-derived antivenoms will still play a critical role for years to come. In this study, we improved the bothropic antivenom (BAv), by capturing toxin-specific antibodies through affinity chromatography using immobilized Bothrops jararaca venom toxins. This process produced an improved antivenom (iBAv) enriched in neutralizing antibodies and depleted of serum proteins. Proteomic analysis showed that iBAv was 87% depleted in albumin and 37-83% lower in other serum proteins compared to BAv. Functional evaluation demonstrated that iBAv had a 2.9-fold higher affinity for venom toxins by surface plasmon resonance and a 2.8-fold lower ED50 in vivo, indicating enhanced potency. Our findings indicate that enriching specific antibodies while depleting serum proteins reduces the total protein dose required and increases the potency of antivenom. Although technical and economic considerations remain for large-scale implementation, this affinity-enriched antivenom represents a significant advancement in improving antivenom efficacy against B. jararaca envenomations.

Glycocalyx Interactions Modulate the Cellular Uptake of Albumin-Coated Nanoparticles

Albumin-based nanoparticles (ABNPs) represent promising drug carriers in nanomedicine due to their versatility and biocompatibility, but optimizing their effectiveness in drug delivery requires understanding their interactions with and uptake by cells. Notably, albumin interacts with the cellular glycocalyx, a phenomenon particularly studied in endothelial cells. This observation suggests that the glycocalyx could modulate ABNP uptake and therapeutic efficacy, although this possibility remains unrecognized. In this study, we elucidate the critical role of the glycocalyx in the cellular uptake of a model ABNP system consisting of silica nanoparticles (NPs) coated with native, cationic, and anionic albumin variants (BSA, BSA+, and BSA-). Using various methodologies-including fluorescence anisotropy, dynamic light scattering, microscale thermophoresis, surface plasmon resonance spectroscopy, and computer simulations─we found that both BSA and BSA+, but not BSA-, interact with heparin, a model glycosaminoglycan (GAG). To explore the influence of albumin-GAG interactions on NP uptake, we performed comparative uptake studies in wild-type and GAG-mutated Chinese hamster ovary cells (CHO), along with complementary approaches such as enzymatic GAG cleavage in wild-type cells, chemical inhibition, and competition assays with exogenous heparin. We found that the glycocalyx enhances the cell uptake of NPs coated with BSA and BSA+, while serving as a barrier to the uptake of NPs coated with BSA-. Furthermore, we showed that harnessing albumin-GAG interactions increases cancer cell death induced by paclitaxel-loaded albumin-coated NPs. These findings underscore the importance of albumin-glycocalyx interactions in the rational design and optimization of albumin-based drug delivery systems.

Insights into the discovery and intervention of metalloproteinase in marine hazardous jellyfish

The proliferation of toxic organisms caused by changes in the marine environment, coupled with the rising human activities along the coastal lines, has resulted in an increasing number of stinging incidents, posing a serious threat to public health. Here, we evaluated the systemic toxicity of the venom in jellyfish Chrysaora quinquecirrha at both cellular and animal levels, and found that jellyfish tentacle extract (TE) has strong lethality accompanied by abnormal elevation of blood biochemical indicators and pathological changes. Joint analysis of transcriptome and proteome indicated that metalloproteinases are the predominant toxins in jellyfish. Specially, two key metalloproteinases DN6695_c0_g3 and DN8184_c0_g7 were identified by mass spectrometry of the red blood cell membrane and tetracycline hydrochloride (Tch) inhibition models. Structurally, molecular docking and kinetic analysis are employed and observed that Tch could inhibit the enzyme activity by binding to the hydrophobic pocket of the catalytic center. In this study, we demonstrated that Tch impedes the metalloproteinase activity thereby reducing the lethal effect of jellyfish, which suggests a potential strategy for combating the health threat of marine toxic jellyfish.

Unveiling hidden toxin diversity: Discovery of novel venom components through manual curation of highly expressed sequences annotated as "no hits" in Phoneutria nigriventer spider venom gland transcriptome

Spider venoms have evolved over thousands of years, optimizing feeding and defense mechanisms. Venom components show pharmacological and biotechnological potential, rising interest in their study. However, the isolation of spider toxins for experimental evaluation poses significant challenges. To address this, transcriptomic analysis combined with computational tools has emerged as an appealing approach to characterizing spider venoms. However, many sequences remain unidentified after automatic annotation. In this study, we manually curated a subset of previously unannotated sequences from the Phoneutria nigriventer transcriptome and identified new putative venom components. Our manual analysis revealed 29 % of the analyzed sequences were potential venom components, 29 % hypothetical/uncharacterized proteins, and 17 % cellular function proteins. Only 25 % of the originally unannotated dataset remained without any identification. Most reclassified components were cysteine-rich peptides, including 23 novel putative toxins. We also found glycine-rich peptides (GRP), corroborating the previous description of GRPs in Phoneutria pertyi venom glands. Furthermore, to emphasize the recurrence of the lack of annotation in spider venom glands transcripts, we provide a survey of the percentage of unidentified sequences in several published spider venom transcriptomics studies. In conclusion, our study highlights the importance of manual curation in uncovering novel venom components and underscores the need for improved annotation strategies to fully exploit the medical and biotechnological potential of spider venoms.

A novel metalloproteinase-derived cryptide from Bothrops cotiara venom inhibits angiotensin-converting enzyme activity

Snake venoms are primarily composed of proteins and peptides, which selectively interact with specific molecular targets, disrupting prey homeostasis. Identifying toxins and the mechanisms involved in envenoming can lead to the discovery of new drugs based on natural peptide scaffolds. In this study, we used mass spectrometry-based peptidomics to sequence 197 peptides in the venom of Bothrops cotiara, including a novel 7-residue peptide derived from a snake venom metalloproteinase. This peptide, named Bc-7a, features a pyroglutamic acid at the N-terminal and a PFR motif at the C-terminal, homologous to bradykinin. Using FRET (fluorescence resonance energy transfer) substrate assays, we demonstrated that Bc-7a strongly inhibits the two domains of angiotensin converting enzyme (Ki < 1 μM). Our findings contribute to the repertoire of biologically active peptides from snake venoms capable of inhibiting angiotensin-converting enzyme (ACE), beyond current known structural motifs and precursors. In summary, we report a novel snake venom peptide with ACE inhibitory activity, suggesting its potential contribution to the hypotensive effect observed in envenomation.

Origins, Technological Advancement, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.

Identification of Peptides in Spider Venom Using Mass Spectrometry

Spider venoms are composed of hundreds of proteins and peptides. Several of these venom toxins are cysteine-rich peptides in the mass range of 3-9 kDa. Small peptides (<3 kDa) can be fully characterized by mass spectrometry analysis, while proteins are generally identified by the bottom-up approach in which proteins are first digested with trypsin to generate shorter peptides for MS/MS characterization. In general, it is sufficient for protein identification to sequence two or more peptides, but for venom peptidomics it is desirable to completely elucidate peptide sequences and the number of disulfide bonds in the molecules. In this chapter, we describe a methodology to completely sequence and determine the number of disulfide bonds of spider venom peptides in the mass range of 3-9 kDa by multiple enzyme digestion, mass spectrometry of native and digested peptides, de novo analysis, and sequence overlap alignment.

Unveiling the peptidome diversity of Lachesismuta snake venom: Discovery of novel fragments of metalloproteinase, l-amino acid oxidase, and bradykinin potentiating peptides

Snake venoms are known to be major sources of peptides with different pharmacological properties. In this study, we comprehensively explored the venom peptidomes of three specimens of Lachesismuta, the largest venomous snake in South America, using mass spectrometry techniques. The analysis revealed 19 main chromatographic peaks common to all specimens. A total of 151 peptides were identified, including 69 from a metalloproteinase, 58 from the BPP-CNP precursor, and 24 from a l-amino acid oxidase. To our knowledge, 126 of these peptides were reported for the first time in this work, including a new SVMP-derived peptide fragment, Lm-10a. Our findings highlight the dynamic nature of toxin maturation in snake venoms, driven by proteolytic processing, post-translational modifications, and cryptide formation.