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Heterologous expression of unknown natural product biosynthetic gene clusters from Streptomyces rapamycinicus and identification of novel meroterpenoids rapamylic acids A-C
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Xuchang YU1, 2, Ruixiang YOU2, Yuzhu WU2, Runze SUN2, Shaoxin CHEN3, Hui WU1, Lei LI2
Acta Microbiologica Sinica | 2025, 65(5) : 2214 - 2228
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Acta Microbiologica Sinica | 2025, 65(5): 2214-2228
• Research Article •
Heterologous expression of unknown natural product biosynthetic gene clusters from Streptomyces rapamycinicus and identification of novel meroterpenoids rapamylic acids A-C
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Xuchang YU1, 2, Ruixiang YOU2, Yuzhu WU2, Runze SUN2, Shaoxin CHEN3, Hui WU1, Lei LI2
Affiliations
  • 1.State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China
  • 2.State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
  • 3.National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, China
Published: 2025-05-04 doi: 10.13343/j.cnki.wsxb.20240802
Outline
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[Objective] Streptomyces rapamycinicus has large biosynthetic potential with 55 natural product biosynthetic gene clusters (BGCs), most of which have not yet been identified. This study aims to obtain a series of novel compounds by Bacterial Artificial Chromosome (BAC) library-based cloning of novel BGCs from S. rapamycinicus on a large scale and then heterologously expressing them in model Streptomyces strains. [Methods] The bioinformatics analysis of the novelty of BGCs screened out 11 unknown BGCs encoding non-ribosomal peptides, polyketides or terpenoids, from S. rapamycinicus SIPI RP202. Then, we cloned these BGCs by constructing a BAC library and screening via PCR, and then introduced them into three heterologous expression hosts by conjugative transfer. Finally, LC-MS was employed to detect whether these BGCs were successfully expressed after fermentation in three media and fermentation broth extraction with two approaches. Novel compounds were separated, purified, and structurally elucidated. [Results] An unknown terpenoid BGC was successfully expressed in Streptomyces albus Del14. Three novel aromatic meroterpenoids, rapamylic acids A-C, were identified. Then, the potential biosynthetic pathways of rapamylic acids A-C were proposed based on their structural features and BGC. [Conclusion] We successfully unlocked a silent BGC from S. rapamycinicus by large-scale BGC cloning and heterologous expression, providing an alternative strategy for the activation of silent BGCs from other Streptomyces strains. Meanwhile, the discovery of this kind of novel meroterpenoids expands the structural diversity of bacterial terpenoids.

Streptomyces rapamycinicus  /  genome mining  /  library construction  /  heterologous expression  /  meroterpenoid
Xuchang YU, Ruixiang YOU, Yuzhu WU, Runze SUN, Shaoxin CHEN, Hui WU, Lei LI. Heterologous expression of unknown natural product biosynthetic gene clusters from Streptomyces rapamycinicus and identification of novel meroterpenoids rapamylic acids A-C[J]. Acta Microbiologica Sinica, 2025 , 65 (5) : 2214 -2228 . DOI: 10.13343/j.cnki.wsxb.20240802
Funding
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  • National Key Research and Development Program of China(2023YFA0916200)
Appendix
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Year 2025 volume 65 Issue 5
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Article Info
doi: 10.13343/j.cnki.wsxb.20240802
  • Receive Date：2024-12-12
  • Online Date：2026-02-05
  • Published：2025-05-04
Article Data
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History
  • Received：2024-12-12
  • Accepted：2025-01-02
Funding
National Key Research and Development Program of China(2023YFA0916200)
Affiliations
    1.State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China
    2.State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
    3.National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, China

Corresponding:

E-mail: LI Lei,
WU Hui,
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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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