Identification and yield improvement of a new rimocidin-producing strain

Abstract:

[Background] Rimocidin is a tetraene macrolide with broad-spectrum antifungal activities, there being developed into a potential agricultural antibiotic. Until now, several Streptomyces producers (such as S.rimosus M527) have been discovered, while the low yield of rimocidin limits the application of these strains in the development of the agricultural antibiotic. [Objective] To systematically reveal the distribution and characteristic of the biosynthetic gene clusters (BGCs) for rimocidin (rim BGCs) in Streptomyces genomes, identify a new strain which can produce rimocidin, and improve its yield via genetic engineering and other strategies. [Methods] We employed BLASTp to search for the homologous proteins of the known synthetases of rimocidin in Streptomyces genomes to discover the strains with predicted rim BGCs and capable of producing rimocidin. The multi-locus sequence analysis (MLSA) was conducted to analyze the phylogenetic relationships among these strains and publicly available Streptomyces strains. A new rimocidin-producing strain was identified based on the metabolite analysis and the titer of rimocidin was increased by medium optimization and RimoR2 overexpression. [Results] A total of 36 Streptomyces strains carrying rim BGCs were predicted, in which S.albofaciens JCM 4342 was capable of producing rimocidin and its congener CE-108. The medium optimization led to a rimocidin titer of 172.5 mg/L. Moreover, the RimoR2 overexpression increased the rimocidin titer by 2.3 folds, which reached 397.1 mg/L. [Conclusion] This study systematically revealed the distribution of rim BGCs in Streptomyces. We confirmed that S.albofaciens JCM 4342 can produce rimocidin and its congener CE-108. Moreover, the titer of rimocidin was improved by genetic engineering. Our findings provide new catalytic elements, strains, and a theoretical basis for the design and construction of strains with high yields of rimocidin and the application and development of rimocidin.