Abstract
Small-molecule metabolites are key pharmaceutical resources embedded in complex organismal metabolomes. Scalable microbial production depends on metabolic activation capacity, which in turn requires efficient genetic variation. Structural variants (SVs), key drivers of phenotypic diversity, are pivotal for organism evolution, yet their highly efficient induction remains challenging. While DNA double-strand breaks (DSBs) facilitate SVs formation, existing mutagenesis technologies struggle to balance high DSB efficiency with cellular preservation, particularly in microbial strain improvement for metabolite production. Conventional irradiation methods suffer from low SVs induction rates, making strain enhancement a lengthy and labor-intensive process. Here, we systematically compare six irradiation technologies in Streptomyces lividans 1326 and identify high-energy pulsed electron beams (HEPE) as an approach which effectively induces strong DSBs while preserving cellular integrity. This results in extensive SVs that reshape genome sequences and 3D chromatin structure, leading to activation of secondary metabolite production. By integrating HEPE with high-throughput metabolomics (HEPE-HiTMS), we discover two secondary metabolites with unusual C-N linkage, respectively. Applied across various microorganisms, HEPE enables record-high clavulanic acid and microcin J25 production, and markedly increases lovastatin yields. With its ability to induce SVs with minimal cytotoxicity, HEPE represents a powerful tool for cryptic metabolite discovery and industrial strain development.
Data availability
Genome and Hi-C sequencing data for S. lividans 1326 and its mutants have been deposited in the NCBI under BioProject PRJNA1264485. RNA sequencing data are available from the NCBI database under accession number GSE315268. Genome sequencing data for S. griseobrunneus and S. fradiae are available via NCBI under accession numbers SAMN45944959 and SAMN45945006. The mass spectrometry-based metabolomics raw data have been deposited in the MassIVE database under accession code MSV000100599. The X-ray crystallographic coordinates for structure reported in this study have been deposited in CCDC under accession number 2432012 [https://www.ccdc.cam.ac.uk/structures/search?id=doi:10.5517/ccdc.csd.cc2mmq00] Source data are provided with this paper.
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Acknowledgements
We thank Professor Linquan Bai at Shanghai Jiao Tong University for discussion and suggestions. This work was supported by the National Key Research and Development Project (2021YFC2100600, F.X).
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X.F., W.W. and F.X. designed the research; X.F., S.Z. and Z.Y. evaluated irradiation methods; X.F. and Z.X. conducted genomic analysis; X.F. and Y.Z. conducted metabolites activation in S. lividans; Z.L. and W.W conducted production enhancement of clavulanic acid; X.F., Y.Z., D.Q., T.H. and J.W. conducted production enhancement of mccJ25; J.X., J.Y. and W.L. conducted production enhancement of lovastatin; X.F. and M.R.S. performed 3D plot analysis; X.F. conducted genetic inactivation, fermentation and compound isolation of novel metabolites; J.Y. and M.W. elucidated compounds structures; M.R.S., W.W. and F.X. wrote the manuscript.
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Feng, X., Li, Z., Zhang, Y. et al. Enhancing microbial metabolic capacity through high-energy electron beam-induced intense structural variations. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69723-3
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DOI: https://doi.org/10.1038/s41467-026-69723-3
