Isolation, identification, and genomic analysis of a prodigiosin-producing strain of Serratia marcescens

Abstract:

[Objective] To select the elite strains among the microorganisms isolated from the rhizosphere of Brassica oleracea var. capitata and evaluate the secondary metabolism potential of the strains, laying a solid foundation for mining the microbial resources in the rhizosphere of this plant. [Methods] The roots of B. oleracea var. capitata were collected from Xiannüshan Town in Wulong District of Chongqing. The conventional methods were then used to isolate microbial strains, and one strain of Serratia marcescens was selected for genome sequencing (PacBio RS II and Illumina HiSeq) and bioinformatic analysis. The antiSMASH was used for the detection and comparison of biosynthetic gene clusters (BGCs) encoding secondary metabolites. Red/ET recombination was employed to capture the BGC for prodigiosin. [Results] One prodigiosin-producing strain of S. marcescens was isolated from the rhizosphere of B. oleracea var. capitata. The genome of this strain contained 11 putative BGCs (1-11) for secondary metabolites, of which 9 BGCs displayed low similarities to the BGCs encoding known compounds. This result suggested that the strain had great potential of producing novel secondary metabolites. Prodigiosin was identified by HPLC and high-resolution mass spectrometry (HRMS). Heterologous expression of BGC4 resulted in the production of prodigiosin in Escherichia coli. Four common promoters were used to drive the expression of BGC in E. coli, and the highest prodigiosin production was observed with the rpoS promoter. [Conclusion] A prodigiosin-producing strain of S. marcescens was isolated from the rhizosphere of B. oleracea var. capitata. The BGC for prodigiosin was captured from the chromosome of this strain and expressed successfully in the surrogate host E. coli BAP1.