Bioinformatics: from Algorithms to Applications 2020

Biologicals based on the entomopathogenic gram-positive bacteria, Bacillus thuringiensis, represent one of the most widespread biopesticides. The potency and specificity of insecticidal action are mostly determined by a set of insecticadial moieties with various activities produced into the crystalline inclusions during the sporulation growth phase of the bacterium. Although some other virulence factors such as chitinases are produced by B. thuringiensis, Cry-toxins refer to the most useful and agriculturally applicable biopesticides. Cry toxins and their subset, 3-D  (three-domain) Cry toxins, not only possess a comprehensive range of affected hosts but also exhibit immense specificity. Unfortunately, an emerging resistance of insects to these toxins due to mutations in host receptor genes retards the progress of fruitful pest management. The two strategies that could contribute to solving this issue are the massive search for the novel toxins and the construction of artificial toxins by means of the domain shuffling. To discover new 3-D Cry toxins in continually appearing genomic data, we developed an HMM-based tool called CryProcessor that allows retrieving sequences of 3-D Cry toxins from large datasets of genetic data and provides an opportunity to get the layout of individual domains. This tool outperforms its analogs in terms of accuracy, speed, and throughput. Cry toxin domain layout provided by CryProcessor, will significantly facilitate the development of chimeric toxins by accelerating in silico construction of chimeric toxins. Considering the diversity of Cry toxins, one generally accepted yet not lucidly validated hypothesis links this diversification of the 3-D Cry toxins with domain exchange between various toxins. However, the only evidence supporting this idea was obtained by a comparison of protein sequences in small groups of the toxins. To fulfill this gap, we conducted a first large-scale phylogenetic study of the 3-D Cry toxins. Using CryProcessor, we screened the IPG and Genbank databases and identified approximately 600 novel toxins, which were then merged with toxins from the Bt-Nomenclature. We then constructed phylogenetic trees based both on full sequences and specific domains. The evaluation of topological differences between the trees revealed a noticeable discrepancy between the topology of the full sequence-based tree and the domain-only trees. We then screened sequences for signals of recombination events. As a result, we revealed 50 recombination events, and it is noteworthy that they belonged to each of the domains. Our results indicate that recombination events represent a pivotal mechanism for the evolution and diversification of 3-D Cry toxins. A clearer understanding of this process and a more in-depth look into the history of recombination events would allow us to develop new specific toxins precisely and efficiently.