Enhancing Microbial Metabolic Capacity through High-Energy Electron Beam-Induced Intense Structural Variations

Enhancing Microbial Metabolic Capacity through High-Energy Electron Beam-Induced Intense Structural Variations | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Enhancing Microbial Metabolic Capacity through High-Energy Electron Beam-Induced Intense Structural Variations Fei Xu, Xinyuan Feng, Zilong Li, Yifei Zhang, Jingping Xu, Zhenguo Xin, and 11 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6603993/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 19 Feb, 2026 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version 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 SV 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 SV induction rates, making strain enhancement a lengthy and labor-intensive process. Here, we systematically compared six irradiation technologies in Streptomyces lividans 1326 and identified high-energy pulsed electron beams (HEPE) as a breakthrough approach, which effectively induces strong DSBs while preserves cellular integrity. This resulted in extensive SVs that reshaped genome sequences and 3D chromatin structure, significantly activating the expression of metabolome profile. By integrating HEPE with high-throughput metabolomics (HEPE-HiTMS), we discovered two novel secondary metabolites with unusual C-N linkage, respectively. Applied across various microorganisms, HEPE also achieved record-high clavulanic acid and microcin J25 production, and markedly increased lovastatin yields. With its ability to induce SVs with minimal cytotoxicity, HEPE represents a transformative tool for cryptic metabolite discovery and industrial strain development. Biological sciences/Microbiology Biological sciences/Biotechnology/Industrial microbiology Biological sciences/Chemical biology/Natural products Full Text Additional Declarations There is NO Competing Interest. Supplementary Files supplementarymaterials.pdf supplementary materials Cite Share Download PDF Status: Published Journal Publication published 19 Feb, 2026 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6603993","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":457657387,"identity":"f8b72dab-6db9-4fce-8d3e-0555bdc8712d","order_by":0,"name":"Fei 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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 SV 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 SV induction rates, making strain enhancement a lengthy and labor-intensive process. Here, we systematically compared six irradiation technologies in Streptomyces lividans 1326 and identified high-energy pulsed electron beams (HEPE) as a breakthrough approach, which effectively induces strong DSBs while preserves cellular integrity. This resulted in extensive SVs that reshaped genome sequences and 3D chromatin structure, significantly activating the expression of metabolome profile. By integrating HEPE with high-throughput metabolomics (HEPE-HiTMS), we discovered two novel secondary metabolites with unusual C-N linkage, respectively. Applied across various microorganisms, HEPE also achieved record-high clavulanic acid and microcin J25 production, and markedly increased lovastatin yields. 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