In silico analysis of koranimine, a cyclic imine compound from Peribacillus frigoritolerans reveals potential nematicidal activity

Abstract

Pine wilt disease (PWD) is a destructive vector-borne forest disease caused by the nematode Bursaphelenchus xylophilus. To date, several options are available for the management of pine wilt disease; however constant development and search for natural products with potential nematicidal activity are imperative to diversify management options and to cope with the possible future emergence of resistance in parasitic nematodes. Here, a combined metabolomics and genomics approach was employed to investigate the chemical repertoire and biosynthetic potential of the bacterial endophyte Peribacillus frigoritolerans BE93, previously characterized to exhibit nematicidal activity against B. xylophilus. Feature-based molecular networking revealed the presence of diverse secondary metabolites. A cyclic imine heptapeptide, koranimine, was found to be among the most abundant secondary metabolites produced. Genome mining displayed the presence of several putative biosynthetic gene clusters (BGCs), including a dedicated non-ribosomal peptide synthase (NRPS) BGC for koranimine. Given the non-ribosomal peptide nature of koranimine, in silico molecular docking analysis was conducted to investigate its potential nematicidal activity against the target receptor ivermectin-sensitive invertebrate α glutamate-gated chloride channel (GluCl). Results revealed the binding of koranimine at the allosteric site of the channel—the ivermectin binding site. Moreover, the ligand-receptor interactions observed were mostly shared between koranimine and ivermectin when bound to the α GluCl receptor thus, suggesting a possibly shared mechanism of potential nematicidal activity. This study highlights the efficiency of combined metabolomics and genomics approach in the identification of candidate compounds.

Peribacillus frigoritoleransT7-IITJ, a potential biofertilizer, induces plant growth-promoting genes ofArabidopsis thaliana

“…This can aid in its plant growth promotion properties and allow its use as a biocontrol agent. Other strains of P. frigoritolerans showed nematicidal and fungicidal activity due to production of koranimine and other compounds, corroborating our results (Montecillo and Bae, 2022b;Y. Wang et al 2022).…”

Isolation and Characterization of Culturable Osmotolerant Microbiota in Hypersaline and Hypergypsic Soils as New Treatment for Osmotic Stress in Plants

“…In summary, it is evident that all of these diverse approaches have the potential to enhance crop performance to some degree under osmotic stress conditions. The obtained results are particularly noteworthy in that all candidate strains significantly improved the germination rate of M. sativa under osmotic stress conditions [99,100]. Overcoming the challenge of germinating many genotypes of this species under stress is a pivotal factor in direct field sowing [100].…”

Culturable Bacterial Endophytes of Wild White Poplar (Populus alba L.) Roots: A First Insight into Their Plant Growth-Stimulating and Bioaugmentation Potential

“…One of the most interesting features of Peribacillus sp. is the production of coranimine, which exhibits nematocidal activity against Bursaphelenchus xylophilus, the causative agent of pine wilt disease [109]; clusters of coranimine biosynthesis are also present in our strains.…”