An RNA sponge directs the transition from feast to famine in Caulobacter crescentus

An RNA sponge directs the transition from feast to famine in Caulobacter crescentus | 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 An RNA sponge directs the transition from feast to famine in Caulobacter crescentus Kathrin Fröhlich, Laura Vogt, Manuel Velasco Gomariz, Malte Siemers, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6224905/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 27 Oct, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract In bacteria, regulatory networks controlling the adaptation of gene expression in response to stress are frequently complemented by base-pairing small regulatory RNAs (sRNAs) that act at the post-transcriptional level. While many regulatory circuits governing stress resilience have been studied in the model bacterium Caulobacter crescentus, only a small fraction of its diverse sRNA repertoire has been characterized. In this study, we globally identified interacting RNA-RNA pairs associated with the major RNA-binding protein Hfq in C. crescentus. In addition to numerous connections between sRNAs and mRNAs, we isolated unconventional pairs consisting of two non-coding sRNAs. Our results indicate that the sRNA CrfA acts as a sponge to inactivate a family of four conserved sRNAs, SisA-D. When induced by carbon starvation, CrfA redirects gene expression towards the utilization of distinct energy sources, and loss of the RNA sponge is linked to a severe growth defect in environments with fluctuating nutrient availability. Biological sciences/Microbiology/Microbial genetics/Bacterial genetics Biological sciences/Molecular biology/Non-coding RNAs/Small RNAs Caulobacter small RNA Hfq RIL-Seq RNA sponge carbon starvation Full Text Additional Declarations There is NO Competing Interest. Supplementary Files VogtVelasco2025NatCommTableS1highconfidencechimeras.xlsx Table S1 VogtVelasco2025NatCommTableS2RNAseqSisACrfADEG.xlsx Table S2 VogtVelasco2025NatCommSourceDataRILseq.xlsx Source Data quantifications nrreportingsummary.pdf Reporting Summary VogtVelascoNatComm2025SI.pdf Supporting Information VogtVelasco2025NatCommSourceData.pdf Source Data Cite Share Download PDF Status: Published Journal Publication published 27 Oct, 2025 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. 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