Genomic characterization for secondary metabolite biosynthetic genes of Microbispora sp. KK1-11
Keywords:
Microbispora, Whole-genome sequence analysis, Actinomycete, Secondary metabolitesAbstract
Background: Rare actinomycetes, especially genus Microbispora, have attracted attention because of their ability to produce various bioactive secondary metabolites. Many valuable secondary metabolites, such as bispolides, linfuranone A, and microbiaeratin, produced by Microbispora spp. have been reported, and there is great interest in efforts to discover new Microbispora spp. with the ability to produce such metabolites. The application of in silico biosynthetic predictions from genome mining data is usually used to identify promising Microbispora spp. in nature. In this study, we used existing genomic data to characterize the taxonomic position of Microbispora sp. KK1-11 and to identify biosynthetic gene clusters (BGCs) in the genome.
Methods: An actinomycete strain KK1-11 was taxonomically characterized using a polyphasic approach. To confirm the taxonomic classification of the strain at the genus level, morphological, chemotaxonomic, and 16S rRNA gene sequence analyses were performed. Whole-genome shotgun sequencing was carried out using an Illumina MiSeq 1TB platform. The genomic data were evaluated for the production of secondary metabolites using the antiSMASH platform and the antibacterial activity of metabolites was also assessed.
Results: Actinomycete strain KK1-11 was taxonomically characterized as a member of the genus Microbispora. Genomic-based identification revealed that while KK1-11 is most closely related to Microbispora catharanthi CR1-09T, the average nucleotide identity value was low at 94.44%. Genome analysis by antiSMASH revealed that KK1-11 contains several secondary metabolite BCGs (smBGCs), including type I and III polyketide synthase, terpene biosynthesis, non-ribosomal peptide synthetase (NRPS), and NRPS-like gene clusters. In addition, several smBGCs in the genome of KK1-11 showed no relatedness to known clusters.
Conclusion: This study demonstrates that Microbispora sp. KK1-11 may represent a novel member of the genus Microbispora capable of producing new secondary metabolites, representing a soil actinomycete with the potential to produce valuable bioactive compounds.
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