Metabolite profiling and genomic properties of an endophytic Bacillus siamensis strain with anti-tumor activity isolated from medicinal plant Curcuma Wenyujin

Plant endophytes produce a variety of secondary metabolites that have a wide range of biological effects. Curcuma wenyujin Y.H. Chen et C. Ling is a medicinal plant of the genus Curcuma in Zingiberaceae possessing anti-tumor effects. However, Bacillus siamensis isolated from C. wenyujin highly remains limited understanding. In this study, a novel B. siamensis named as WYJ-E14 strain from C. wenyujin was isolated. The CCK8 assay showed that the metabolites produced by WYJ-E14 strain significantly inhibited the growth of melanoma and glioma cells. Metabolomic analysis showed that the eight metabolites of the WYJ-E14 metabolites had anti-tumor cell growth activity, including desferrioxamine G1, surfactin, menaquinone-4, tracheloside, proscillaridin, microcolin J, stevioside, and demethoxycurcumin. Genomic sequencing displayed that the whole genome of WYJ-E14 contained a circular chromosome with a total length of 4,020,075 bp, and had no plasmid. Genome annotation identified 4008 putative protein-coding genes, 1 tRNA, and 27 rRNAs. The CDSs number assigned to the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and Clusters of Orthologous Genes databases were 2145, 2764 and 3403, respectively. Biosynthetic gene clusters (BGCs) related to the synthesis of surfactin, difficidin, fengycin, bacillaene, macrolactin, butirosin A/butirosin B, bacillibactin and bacilysin were identified in the genome of WYJ-E14 by antiSMASH analysis. Most importantly, the genes involved in the biosynthesis of surfactin and menaquinone-4 metabolism were identified. In addition, WYJ-E14 genome also contained sequences that shared similarity with the genes encoding enzymes involved in the plant curcumin anabolism. The predicted ORFs encoded 120 secretory proteins. Comparative genome analysis showed that WYJ-E14 possessed collinear region among B. siamensis YB-1631 and B. velezensis W1. Taken together, this work offered a foundation for function study of target genes, and facilitated a genetic engineering of B. siamensis WYJ-E14 to improve agricultural and biomedical applications.