Modern venomics-Current insights, novel methods, and future perspectives in biological and applied animal venom research

Abstract

Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit.

Keywords: antivenom; bioassays; envenomation; evolution; genomics; modern venomics; spatial -omics; toxin production; translational research; venom.

Figure 1:

The importance and impact of venom. The biology and ecology of venomous species prompt diversity of venoms, which are constituted of highly specific toxin components that were adaptively produced over time. Predator-prey interactions are major evolutionary forces that often trigger arms races of venom toxicity and resistance. Extrinsic factors that affect venomous species and their interaction with humans include species expansion or decline (linked to the biodiversity crisis and climate change) but also the increasing human growth and migration. Basic venom research investigates why and how venoms and toxin genes evolve based on modern “omics” methods. Translational research exploits these basic studies for developing various applications, ranging from pharmacology (e.g., anti-pain and anti-cancer drugs, diagnostic markers, antivenom development) to agrochemistry (pesticides, antiparasitic compounds for crop and livestock protection) and biotechnology (e.g., nanopore sensing).

Figure 2:

Studied venomous metazoan species and available venom proteins. The numbers of studied venomous metazoans and their reviewed venom proteins that are provided in UniProt's animal venom database (ToxProt) are illustrated. Accessed on 1 April 2022, we mined 7,230 entries for venomous species. Venom protein numbers are only given for the larger taxonomic groups; the red circles are proportional to each other. Only taxa with a described venom protein are included; other metazoan species are pruned. The blue circles that show the species numbers are in proportion to each other.

Figure 3:

The major interdisciplinary research areas in venomics. The basic, interlinked, modern research fields in venomics are shown in the first row, and linked through simplified workflows with the final output(s). The main applied and evolutionary questions addressed are shown in the bottom, and integrated in the relevant topics. The flow diagrams that connect most research areas with each other illustrate the highly integrative nature of modern venomics. FISH: fluorescence in situ hybridization.

Figure 4:

The integration of proteomics, transcriptomics, and genomics in venom research. The general workflow for proteomics is shown on the left. Transcriptome analysis steps are illustrated in the middle. Please note that for state-of-the-art genomics multiple RNA samples from both sexes and different tissues (not only venom glands) are sequenced to perform differential gene expression analyses and to predict gene models more precisely. The genome sequencing steps are condensed and focused on the RNA read mapping. For more details please refer to the references given in the text. cDNA: complementary DNA; HMW: high molecular weight; ONT: Oxford Nanopore Technologies; PacBio: Pacific Biosciences.

Figure 5:

The integration of -omics-based research to improve translational research but also our basic understanding of venom and toxin gene evolution. (A) Shows the biological process from gene to protein; (B) illustrates genome editing aspects to investigate toxin evolution, function, adaptive value, spatio-temporal variability, and ontogenetic fate; (C) summarizes the major steps in translational research, from bioprospecting to application. PTMs: posttranslational modifications.

Figure 6.

Approaches to study the activity of venom components span from in vivo, ex vivo, and in vitro to in silico methods. This allows the characterization of a broad spectrum of physiological effects, from whole-organism phenotype to molecular target.

Figure 7.

Schematic representation of nanopore biosensing. (A) Nanopore biosensing uses minute changes in electric current caused by the translocation of an analyte through the pore; each analyte is characterized by the percentage of current blockage and its duration. (B) The most widely used application of nanopore biosensing is DNA/RNA sequencing. The present trace is adapted from [312].