Genome mining and In‐silico determination of secondary metabolites of bacteria against Fusarium oxysporum f. sp. Lycopersici

Abstract

AbstractFusarium wilt caused by Fusarium oxysporum f. sp. lycopersici (FOL) is a devastating global plant fungal disease particularly in tomatoes leading to serious economic losses. The aim of this study was to determine an in silico effective antifungal metabolite against two important FOL proteins. An in silico ligand–protein interaction was carried out by genome mining and molecular docking of the best ligand‐producing strains of bacteria using AutoDock and antiSMASH tools. The secondary metabolites obtained from different bacteria selected for biocontrol agents (BCA) were docked against SIX and TOM proteins. The selected compounds were docked in the active site of both proteins while random starting positions, torsion angles were established for all ligands. Based on the protein–ligand interactions, the best inhibitor of SIX and TOM protein was xanthobaccine A from Lysobacter sp. strain SB‐K88. On the other hand, the best BCAs compound was heat‐stable antifungal factor obtained from L. enzymogenes, viginiafactin (Pseudomonas sp. QS1027), massetolide A (P. fluorescenss 5101), bicorlnutin A1 and A2 (Xenorhabdus budapestensis) which showed similarity scores viz., 1.25 (with domain NRP, Polyketide), 1.09 (NRP domain), 1.06(NRP domain), 1.00 (NRP domain). The results of our findings suggest Lysobacter sp. as a good biocontrol agent with active biosynthetic gene clusters and as a suitable substitute for agrochemicals. The output of this study will be useful in future management of F. oxysporum f. sp. lycopersici with other plant pathogen and help in crop improvement.