The domain exchange between 3‐domain Cry toxins contributes to their diversity and specificity

Abstract

Spore-forming bacteria Bacillus thuringiensis (Bt) can infect a wide range of invertebrate hosts efficiently and specifically; therefore, it is extensively implemented in ecological biopesticide production. This phenomenon is primarily explained by the presence of highly diversified crystalliferous Cry-toxins embedded in spores; however, the exact underlying causes of these toxins' divergence remains speculative. Nonetheless, understanding these natural mechanisms could provide insights into constructing artificial insecticidal moieties, which is highly demanded due to the sporadic occurrence of resistance in pests. Three-domain Cry toxins (3-D) represent the most abundant class of Cry toxins sharing similar structural features yet are immensely diverse in sequence identity. The latter leads to the absence of thorough phylogenetic studies involving these toxins on a large-scale, and we have attempted to fill this gap. We started with gathering Cry toxin sequences from all publicly available data sources, including Bt- genome assemblies, the Genbank database, and the Bt-nomenclature. After searching for 3-D toxins followed by deduplication, we obtained 370 toxins, for which phylogenetic trees were reconstructed based on individual domains and full-length toxins. A striking dissimilarity between their topologies (which was most evident for the third domain) has allowed us to infer that the domains' evolution is somehow independent and also supported the hypothesis that the emergence of the new toxins is orchestrated by shifts of the third domain between sequences. We next ran the RDP (Recombination Detection Protocol) program, searching for recombination events. As a result, we observed more than 70 events. In other words, almost every fourth toxin is formed after the onset of the recombination event. Two-third of the domain exchanges related to the third domain; nevertheless, exchanges affected all three domains. That observation substantially extends the former hypothesis. Finally, we assessed detected events for functional significance. Not only were the events characterized by a remarkable effect on the evolutionary selection (with significant signals of positive selection), but recombination led to alterations in host specificity for several events. All things considered, we have drawn a conclusion that the domain exchange is one of the primary mechanisms underlying the emergence and specificity of Cry toxins. This observation has a potential practical implementation in using in silico experiments to construct novel artificial biopesticides.