Analysis of the potential associated with the siderophores synthesis in the Bacillus subtilis strain using whole genome sequencing

Abstract

T.P. Dunyashev*, V.H. Melikidy, E.A. Brazhnik, S.N. Bikonya, N.V. Tarlavin, A.V. Dubrovin, D.G. Tiurina, V.A. Filippova, L.A. Ilina, E.A. Yildirim, G.Yu. Laptev and A.V. Platonov

The use of biological products based on beneficial microorganisms that produce siderophores, which reduce the concentration of available to pathogensiron ions, can be successfully used in agriculture. The aim of our study was the sequencingand functional annotation of the genome of Bacillus subtilis strain from the collection of BIOTROF Ltd to identify genes associated with the synthesis of siderophores. Nucleotide sequences were analyzed using a MiSeq instrument (Illumina, Inc., USA) together with a MiSeq Reagent Kit v3 (300-cycle) (Illumina, Inc., USA). Functional genome annotation was carried out using the PROKKA 1.12 (https://github.com/kbaseapps/ProkkaAnnotation http://vicbioinformatics.com/) and RAST 2.0 (https://rast.nmpdr.org) programs. The KEGG Pathway database was used to assess the pool of genes associated with antimicrobial activity and construct a metabolic map (http://www.genome.jp/kegg/). When carrying out bioinformatic processing of whole genome sequencing data of the B. subtilis strain, several gene clusters associated with the synthesis of siderophores were identified. Аlmost all genes necessary for the implementation of the process of iron binding with the participation of bacillibactin were found. A cluster of DhbA, DhbB, DhbC genes associated with the production of enzymes 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (EC 1.3.1.28), isochorismatase (EC 3.3.2.1) and isochorismates synthase (EC 5.4.4.2), which are responsible for synthesis of bacillibactin precursor was found. The cluster of genes FeuA, FeuB, FeuC, and FeuD is associated with the synthesis of substrate-binding proteins of the iron transport system. In the genome of B. subtilis, genes associated with the synthesis of other siderophores were also found-enterochelin, described for E. coli and Campylobacter coli, alsomyxochelin A, first found in Angiococcus disciformis. It is likely that B. subtilis bacteria can synthesize several synergistic siderophores to increase their competitiveness. In our opinion, there is a potential for using the B. subtilis strain in animal husbandry and plant growing as a basis for bacterial biopreparations-producers of siderophores, in order to reduce the pathogenic load.

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