Comparative transcriptomic analysis of two Saccharopolyspora spinosa strains reveals the relationships between primary metabolism and spinosad production

Yunpeng Zhang,Tie Yin,Kexue Huang,Qi Li,Qiulong Zou,Dongsheng Guo,Xiaolin Zhang,Xiaomeng Liu

doi:10.1038/s41598-021-94251-z

Abstract

Saccharopolyspora spinosa is a well-known actinomycete for producing the secondary metabolites, spinosad, which is a potent insecticides possessing both efficiency and safety. In the previous researches, great efforts, including physical mutagenesis, fermentation optimization, genetic manipulation and other methods, have been employed to increase the yield of spinosad to hundreds of folds from the low-yield strain. However, the metabolic network in S. spinosa still remained un-revealed. In this study, two S. spinosa strains with different spinosad production capability were fermented and sampled at three fermentation periods. Then the total RNA of these samples was isolated and sequenced to construct the transcriptome libraries. Through transcriptomic analysis, large numbers of differentially expressed genes were identified and classified according to their different functions. According to the results, spnI and spnP were suggested as the bottleneck during spinosad biosynthesis. Primary metabolic pathways such as carbon metabolic pathways exhibited close relationship with spinosad formation, as pyruvate and phosphoenolpyruvic acid were suggested to accumulate in spinosad high-yield strain during fermentation. The addition of soybean oil in the fermentation medium activated the lipid metabolism pathway, enhancing spinosad production. Glutamic acid and aspartic acid were suggested to be the most important amino acids and might participate in spinosad biosynthesis.

Highlights

Saccharopolyspora spinosa is a well-known actinomycete for producing the secondary metabolites, spinosad, which is a potent insecticides possessing both efficiency and safety
As the fermentation stage comes to the stationary phase, the cell growth stopped, while the spinosad biosynthesis continued
The yield of spinosad in the samples were evaluated by HPLC, which indicated that the production of spinosad in S. spinosa S3-3 was 6–16 times higher than that in S. spinosa ATCC_49460 at these three time points (Figure S1)

Summary

Introduction

Saccharopolyspora spinosa is a well-known actinomycete for producing the secondary metabolites, spinosad, which is a potent insecticides possessing both efficiency and safety. SpnI and spnP were suggested as the bottleneck during spinosad biosynthesis Primary metabolic pathways such as carbon metabolic pathways exhibited close relationship with spinosad formation, as pyruvate and phosphoenolpyruvic acid were suggested to accumulate in spinosad high-yield strain during fermentation. Spinosyns biosynthesis are localized in a large genomic region spanning 74 kilo-base in length in S. spinosa genome[8,9,10,11,12,13]. In this ideal genomic region, five large genes, spnA, B, C, D and E, encode a type I polyketide synthase, which controls the biosynthesis of the carbon skeleton of spinosyns[8]. The primary metabolism pathways, including fatty acid degradation, redox controlling and so on, have been considered to have a relationship with the production of spinosad[13,29,30,31]

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Results

Discussion

Conclusion