Flaviolin-Like Gene Cluster Deletion Optimized the Butenyl-Spinosyn Biosynthesis Route in Saccharopolyspora pogona

CRISPRi-mediated multigene downregulating redirects the metabolic flux to spinosad biosynthesis in Saccharopolyspora spinosa

Microorganisms are often likened to complex production workshops. In Saccharopolyspora spinosa (S. spinosa), the biosynthesis of spinosad is a production line within its intricate workshop. Optimizing the entire production environment and reducing unnecessary metabolic flow is essential to increasing spinosad yield. Pyruvate serves as a crucial precursor for spinosad biosynthesis. Previous studies revealed that the pyc gene is highly expressed in the gluconeogenic pathway, leading to a pyruvate shunt. By downregulating pyc, we enhanced spinosad yield, although the improvement was below expectations. We speculated that most of the accumulated pyruvate following the pyc knockdown entered some synthetic pathways unrelated to spinosad. Through metabolic pathway and qRT-PCR analyses, we found that the expression levels of gltA1 and atoB3 within the pyruvate metabolic tributary, including the TCA cycle and ethylmalonyl-CoA pathway, were significantly increased in the pyc knockdown strain. The combined knockdown of these three genes optimized the spinosad production line, increasing its yield to 633.1 ± 38.6 mg/L, representing a 199.4 % increase. This study identifies three key genes for optimizing spinosad biosynthesis and offers insights into gene screening and the efficient construction of Spinosad-producing strains.

Improving butenyl-spinosyn production in Saccharopolyspora pogona through combination of metabolic engineering and medium optimization

Butenyl-spinosyn is a high-quality biological insecticide produced by Saccharopolyspora pogona that effectively targets a broad range of insect pests. However, the large-scale production of this insecticide is hindered by its low yield. Herein, based on prior comparative genomic analysis, five mutations were individually overexpressed in aG6. Subsequently, the combinatorial overexpression of sp1322 (encoding NAD-glutamate dehydrogenase) and sp6746 (encoding dTDP-glucose 4,6-dehydratase) in aG6 resulted in strain O1322-6746. The production of butenyl-spinosyn in O1322-6746 was 77.1% higher than that in aG6. Comparative targeted metabolomic analysis uncovered that O1322-6746 exhibited increased metabolic flux toward butenyl-spinosyn precursors. Furthermore, single-factor experiments, Plackett-Burman analysis and response surface methodology were performed to optimize the fermentation medium for O1322-6746. Ultimately, butenyl-spinosyn production was enhanced to 298.5 mg/L in a 5-L bioreactor, marking the highest yield ever reported. This work demonstrated that combining metabolic engineering with medium optimization is an effective strategy to improve butenyl-spinosyn production.

Addition of vegetable oil to enhance the biosynthesis of butenyl-spinosyn in a high production strain Saccharopolyspora pogona

Butenyl-spinosyn discovered from Saccharopolyspora pogona, is a broad-spectrum bioinsecticide. In order to further improve the production, the fermentation medium of a high-production strain Sa. pogona ASAGF30A11 obtained by mutagenesis, was optimized by adding different species and concentrations vegetable oil. In our study, the effect of peanut oil on the growth and production was proved by monitoring the growth curves, key gene transcription level and content of acyl-CoA. After adding 10 g/L of peanut oil, the additional carbon sources redirected the carbon flux toward strain growth, inhibiting the synthesis of butenyl-spinosyn, while increasing biomass by approximately 1.5-fold. However, when adding 1 g/L of peanut oil, it functions as a surfactant, greatly promoting the synthesis of butenyl-spinosyn, resulting in a 1.52-fold increase in production. The research provides a promising strategy to improve butenyl-spinosyn production.

The PurR family transcriptional regulator promotes butenyl-spinosyn production in Saccharopolyspora pogona

Butenyl-spinosyn, derived from Saccharopolyspora pogona, is a broad-spectrum and effective bioinsecticide. However, the regulatory mechanism affecting butenyl-spinosyn synthesis has not been fully elucidated, which hindered the improvement of production. Here, a high-production strain S. pogona H2 was generated by Cobalt-60 γ-ray mutagenesis, which showed a 2.7-fold increase in production compared to the wild-type strain S. pogona ASAGF58. A comparative transcriptomic analysis between S. pogona ASAGF58 and H2 was performed to elucidate the high-production mechanism that more precursors and energy were used to synthesize of butenyl-spinosyn. Fortunately, a PurR family transcriptional regulator TF00350 was discovered. TF00350 overexpression strain RS00350 induced morphological differentiation and butenyl-spinosyn production, ultimately leading to a 5.5-fold increase in butenyl-spinosyn production (141.5 ± 1.03 mg/L). Through transcriptomics analysis, most genes related to purine metabolism pathway were downregulated, and the butenyl-spinosyn biosynthesis gene was upregulated by increasing the concentration of c-di-GMP and decreasing the concentration of c-di-AMP. These results provide valuable insights for further mining key regulators and improving butenyl-spinosyn production. KEY POINTS: • A high production strain of S. pogona H2 was obtained by 60Co γ-ray mutagenesis. • Positive regulator TF00350 identified by transcriptomics, increasing butenyl-spinosyn production by 5.5-fold. • TF00350 regulated of butenyl-spinosyn production by second messengers.

Genome Combination Improvement Strategy Promotes Efficient Spinosyn Biosynthesis in Saccharopolyspora spinosa

Spinosyns are secondary metabolites produced by Saccharopolyspora spinosa known for their potent insecticidal properties and broad pesticidal spectrum. We report significant advancements in spinosyn biosynthesis achieved through a genome combination improvement strategy in S. spinosa. By integrating modified genome shuffling with ultraviolet mutation and multiomics analysis, we developed a high-yield spinosyn strain designated as YX2. The levels of most proteins and metabolites linked to primary metabolism and spinosyn biosynthesis were greater in this strain than those in S. spinosa. Based on these insights, we overexpressed 15 relevant functional genes to enhance the conversion of fatty acids into acetyl-coenzyme A. Notably, the overexpression of acd (YX2_3432) significantly increased the spinosyn yield, reaching 1120 ± 108 mg/L, which is about 12 times higher than that produced by S. spinosa. This study presents a valuable and straightforward strategy that can be broadly applied to enhance the production of secondary metabolites in actinomycetes.

Application and research progress of ARTP mutagenesis in actinomycetes breeding

Atmospheric and room temperature plasma (ARTP) is an emerging artificial mutagenesis breeding technology. In comparison to traditional physical and chemical methods, ARTP technology can induce DNA damage more effectively and obtain mutation strains with stable heredity more easily after screening. It possesses advantages such as simplicity, safety, non-toxicity, and cost-effectiveness, showing high application value in microbial breeding. This article focuses on ARTP mutagenesis breeding of actinomycetes, specifically highlighting the application of ARTP mutagenesis technology in improving the performance of strains and enhancing the biosynthetic capabilities of actinomycetes. We analyzed the advantages and challenges of ARTP technology in actinomycetes breeding and summarized the common features, specific mutation sites and metabolic pathways of ARTP mutagenic strains, which could give guidance for genetic modification. It suggested that the future research work should focus on the establishment of high throughput rapid screening methods and integrate transcriptomics, proteomics, metabonomics and other omics to delve into the genetic regulations and synthetic mechanisms of the bioactive substances in ARTP mutated actinomycetes. This article aims to provide new perspectives for actinomycetes breeding through the establishment and application of ARTP mutagenesis technology, thereby promoting source innovation and the sustainable industrial development of actinomycetes.

Combinatorial metabolic engineering strategy of precursor pools for the yield improvement of spinosad in Saccharopolyspora spinosa

Spinosad is an insecticide produced by Saccharopolyspora spinosa, and its larvicidal activity is considered a promising approach to combat crop pests. The aim of this study was to enhance the synthesis of spinosad through increasing the supply of acyl-CoAs precursor by the following steps. (i) Engineering the β-oxidation pathway by overexpressing key genes within the pathway to promote the synthesis of spinosad. The results showed that the overexpression of fadD, fadE, and fadA1 genes, as well as the co-expression of fadA1 and fadE genes, increased the yield of spinosad by 0.36-fold, 0.89-fold, 0.75-fold and 1.25-fold respectively. (ii) Employing combinatorial engineering of the β-oxidation pathway and ACC/PCC pathway to promote the synthesis of spinosad. The results showed that the co-expression of fadE and pccA, as well as accC and fadE, resulted in a 1.77-fold and 1.43-fold increase in spinosad production respectively. (iii) When exogenous triacylglycerol was added to the fermentation medium, the solely engineering of the β-oxidation pathway increased the yield of spinosad by 7.13-fold, reaching 427.23 mg/L. While the combinatorial engineering of both the β-oxidation pathway and ACC/PCC pathway increased the yield of spinosad by 9.61-fold, reaching 625.17 mg/L, and further optimization of the culture medium resulted in an even higher yield of spinosad, reaching 1293.43 mg/L. The results of this study indicate that the above combination strategy can promote the efficient biosynthesis of spinosad.

Mechanistic insight for improving butenyl-spinosyn production through combined ARTP/UV mutagenesis and ribosome engineering in Saccharopolyspora pogona

Butenyl-spinosyn is a highly effective, wide-spectrum and environmentally-friendly biological insecticide produced by Saccharopolyspora pogona. However, its scale-up is impeded due to its lower titer in wild-type strains. In this work, ARTP/UV mutagenesis and ribosome engineering were employed to enhance the butenyl-spinosyn production, and a stable mutant Saccharopolyspora pogona aG6 with high butenyl-spinosyn yield was successfully obtained. For the first time, the fermentation results in the 5 L bioreactor demonstrated that the butenyl-spinosyn produced by mutant Saccharopolyspora pogona aG6 reached the maximum value of 130 mg/L, almost 4-fold increase over the wild-type strain WT. Furthermore, comparative genomic, transcriptome and target metabolomic analysis revealed that the accumulation of butenyl-spinosyn was promoted by alterations in ribosomal proteins, branched-chain amino acid degradation and oxidative phosphorylation. Conclusively, the proposed model of ribosome engineering combined with ARTP/UV showed the improved biosynthesis regulation of butenyl-spinosyn in S. pogona.

Effects of a Pirin-like protein on strain growth and spinosad biosynthesis in Saccharopolyspora spinosa

Pirin family proteins perform a variety of biological functions and widely exist in all living organisms. A few studies have shown that Pirin family proteins may be involved in the biosynthesis of antibiotics in actinomycetes. However, the function of Pirin-like proteins in S. spinosa is still unclear. In this study, the inactivation of the sspirin gene led to serious growth defects and the accumulation of H2O2. Surprisingly, the overexpression and knockout of sspirin slightly accelerated the consumption and utilization of glucose, weakened the TCA cycle, delayed sporulation, and enhanced sporulation in the later stage. In addition, the overexpression of sspirin can enhance the β-oxidation pathway and increase the yield of spinosad by 0.88 times, while the inactivation of sspirin hardly produced spinosad. After adding MnCl2, the spinosad yield of the sspirin overexpression strain was further increased to 2.5 times that of the wild-type strain. This study preliminarily revealed the effects of Pirin-like proteins on the growth development and metabolism of S. spinosa and further expanded knowledge of Pirin-like proteins in actinomycetes. KEY POINTS: • Overexpression of the sspirin gene possibly triggers carbon catabolite repression (CCR) • Overexpression of the sspirin gene can promote the synthesis of spinosad • Knockout of the sspirin gene leads to serious growth and spinosad production defects.