Disruption of ribosomal hibernation increases translational capacity in diverse microbial hosts

Disruption of ribosomal hibernation increases translational capacity in diverse microbial hosts | 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 Disruption of ribosomal hibernation increases translational capacity in diverse microbial hosts Jair Diaz-Ramirez, Aaron Miranda-Neri, Rafael Díaz-Méndez, Paul Rosas-Santiago, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7255729/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract Ribosome hibernation factors (RHFs) inactivate ribosomes under stress to promote survival but limit biosynthetic capacity. While essential in fluctuating natural environments, this mechanism restricts productivity in laboratory and industrial settings. We found RHFs expression inversely correlates with growth rate and heterologous protein production, revealing a trade-off between stress adaptation and biosynthesis. Our physiological characterization showed broad fitness gains in Δ rmf strains across 95 carbon sources, whereas Δ raiA mutants exhibited variable, condition-dependent effects, indicating distinct roles. RHFs promoter activity varied with nutrient availability, displaying transient expression in rich media and sustained activity under poor carbon sources, highlighting ribosomal hibernation’s role in nutrient limitation. Deletion of raiA and rmf in E. coli increased translation, boosting heterologous protein and metabolite yields. Transcriptomics of Δ raiA revealed a shift from stress-responsive to growth-promoting programs. Extending this approach, RHFs inactivation enhanced protein production in Pseudomonas putida and Saccharomyces cerevisiae , establishing ribosomal hibernation as a broadly engineerable target to enhance microbial production. Biological sciences/Molecular biology/Translation Biological sciences/Chemical biology/Synthetic biology Escherichia coli synthetic biology ribosomal hibernation factors indigoidine proteomic budget Full Text Additional Declarations The authors declare no competing interests. Supplementary Files SupplementaryTables.xlsx Supplementary Tables Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions 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. 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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-7255729","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":496308100,"identity":"69e18bc3-cde3-47dd-9c22-470cd4f29d9e","order_by":0,"name":"Jair Diaz-Ramirez","email":"","orcid":"","institution":"National Autonomous University of Mexico","correspondingAuthor":false,"prefix":"","firstName":"Jair","middleName":"","lastName":"Diaz-Ramirez","suffix":""},{"id":496308101,"identity":"bfbb8d67-6fb8-4b4e-b709-c1b5a50741dd","order_by":1,"name":"Aaron Miranda-Neri","email":"","orcid":"","institution":"National Autonomous University of 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While essential in fluctuating natural environments, this mechanism restricts productivity in laboratory and industrial settings. We found RHFs expression inversely correlates with growth rate and heterologous protein production, revealing a trade-off between stress adaptation and biosynthesis. Our physiological characterization showed broad fitness gains in Δ\u003cem\u003ermf\u003c/em\u003e strains across 95 carbon sources, whereas Δ\u003cem\u003eraiA\u003c/em\u003e mutants exhibited variable, condition-dependent effects, indicating distinct roles. RHFs promoter activity varied with nutrient availability, displaying transient expression in rich media and sustained activity under poor carbon sources, highlighting ribosomal hibernation’s role in nutrient limitation. Deletion of \u003cem\u003eraiA\u003c/em\u003e and \u003cem\u003ermf \u003c/em\u003ein \u003cem\u003eE. coli\u003c/em\u003e increased translation, boosting heterologous protein and metabolite yields. 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