A rational nomenclature for naming peptide toxins from spiders and other venomous animals
Introduction
Scientists and lay public alike have been interested in the secretions from venomous animals for many centuries. However, the modern era of molecular toxinology did not begin until the 1960s and it was driven primarily by a desire to purify and understand the mechanism of action of lethal components from medically important animals such as marine cone snails (Whysner and Saunders, 1966), stonefish (Deakins and Saunders, 1967), and snakes (Sato et al., 1969).
The pioneering work of Baldomero Olivera, Michael Adams, Lourival Possani and others in the late 1980s and early 1990s led to the realization that most animal venoms comprise a complex cocktail of peptide and protein components of which the lethal toxin often represents only a minor proportion (Olivera, 1997, Possani et al., 2000, Adams, 2004). Moreover, it gradually became clear that many of the non-lethal venom components have useful bioactivities that enable them to be deployed as research tools, such as in the characterization of ion channels (Adams et al., 1993, McIntosh et al., 1999a, King, 2007, King, 2008), or as leads for the development of pharmaceutical agents (Harvey, 2002, Lewis and Garcia, 2003) and insecticides (Tedford et al., 2004b, Bosmans and Tytgat, 2007). This realization, combined with the development of more sophisticated venom fractionation techniques, advances in mass spectrometry (Escoubas, 2006, Favreau et al., 2006, Escoubas et al., 2008), and the ability to directly analyze toxin transcripts from venom-gland cDNA libraries (Kozlov et al., 2005, Sollod et al., 2005), has led to a rapid increase in rate of peptide-toxin discovery during the past decade.
Unfortunately, this rapid expansion of the peptide-toxin database has not been matched by the development of a rational nomenclature for naming these toxins. In this article, we demonstrate that the number of peptide-toxin sequences being deposited in the protein and nucleic acid databases is growing exponentially, with the result that continued use of ad hoc naming schemes will introduce confusion and make it difficult to compare toxins and establish evolutionary relationships. We have therefore developed a rational nomenclature that imparts each toxin name with information about its origin and biological activity. We suggest that this nomenclature can be applied to the naming of peptide toxins from spiders and other venomous animals.
Section snippets
Growth of the peptide-toxin database
We define peptide toxins as venom peptides with a molecular mass less than 10 kDa, which includes the vast majority of proteinaceous toxins from spiders, hymenopterans, cone snails, and scorpions (and a significant proportion of sea anemone and snake toxins). This cut-off value provides a clear distinction between the peptide toxins that dominate most animal venoms and larger enzymes and haemostatic factors from snakes, for which an established nomenclature already exists (Meier and Stocker, 1992
Conclusions
We have devised a simple, rational nomenclature for naming peptide toxins that conveys each toxin name with information about the biological origin of the peptide, its molecular target, and its relationship to known paralogs and orthologs. Although there will inevitably be some resistance to revising toxin names that have been in use for some time, it should be emphasized that systematic revision of toxin names at this point in time, with less than 1500 sequences in the Tox-Prot database, is
Acknowledgements
We thank Paul Alewood for comments on the manuscript, and we acknowledge financial support from the Australian Research Council (Discovery Grants DP0774245 to GFK and DP0559396 to GMN/GFK), the Australian Department of Education Science & Technology (International Linkage Grant FR50106 to GMN/PE), and the Centre National de la Recherche Scientifique (Projets Internationaux de Coopération Scientifique Grant to PE/GMN). We dedicate this manuscript to our inspirational friend and colleague, Prof.
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