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

Author

Listed:
  • Laura N. Vogt

    (Friedrich Schiller University)

  • Manuel Velasco Gomariz

    (Friedrich Schiller University)

  • Malte Siemers

    (Friedrich Schiller University
    Friedrich Schiller University)

  • Kai Papenfort

    (Friedrich Schiller University
    Friedrich Schiller University)

  • Kathrin S. Fröhlich

    (Friedrich Schiller University
    Friedrich Schiller University)

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 identify 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 also recover RNA-RNA pairs consisting of two non-coding transcripts. 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.

Suggested Citation

  • Laura N. Vogt & Manuel Velasco Gomariz & Malte Siemers & Kai Papenfort & Kathrin S. Fröhlich, 2025. "An RNA sponge directs the transition from feast to famine in Caulobacter crescentus," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-65274-1
    DOI: 10.1038/s41467-025-65274-1
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    References listed on IDEAS

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    1. Daniel G. Mediati & Julia L. Wong & Wei Gao & Stuart McKellar & Chi Nam Ignatius Pang & Sylvania Wu & Winton Wu & Brandon Sy & Ian R. Monk & Joanna M. Biazik & Marc R. Wilkins & Benjamin P. Howden & T, 2022. "RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Michaela Huber & Anne Lippegaus & Sahar Melamed & Malte Siemers & Benjamin R. Wucher & Mona Hoyos & Carey Nadell & Gisela Storz & Kai Papenfort, 2022. "An RNA sponge controls quorum sensing dynamics and biofilm formation in Vibrio cholerae," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Hervé Celia & Nicholas Noinaj & Stanislav D. Zakharov & Enrica Bordignon & Istvan Botos & Monica Santamaria & Travis J. Barnard & William A. Cramer & Roland Lloubes & Susan K. Buchanan, 2016. "Structural insight into the role of the Ton complex in energy transduction," Nature, Nature, vol. 538(7623), pages 60-65, October.
    4. Daniel G. Mediati & Julia L. Wong & Wei Gao & Stuart McKellar & Chi Nam Ignatius Pang & Sylvania Wu & Winton Wu & Brandon Sy & Ian R. Monk & Joanna M. Biazik & Marc R. Wilkins & Benjamin P. Howden & T, 2022. "Publisher Correction: RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance," Nature Communications, Nature, vol. 13(1), pages 1-1, December.
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