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An RNA sponge controls quorum sensing dynamics and biofilm formation in Vibrio cholerae

Author

Listed:
  • Michaela Huber

    (Friedrich Schiller University Jena, Institute of Microbiology)

  • Anne Lippegaus

    (Friedrich Schiller University Jena, Institute of Microbiology)

  • Sahar Melamed

    (Eunice Kennedy Shriver National Institute of Child Health and Human Development
    The Hebrew University of Jerusalem)

  • Malte Siemers

    (Friedrich Schiller University Jena, Institute of Microbiology
    Friedrich Schiller University Jena)

  • Benjamin R. Wucher

    (Dartmouth College)

  • Mona Hoyos

    (Friedrich Schiller University Jena, Institute of Microbiology)

  • Carey Nadell

    (Dartmouth College)

  • Gisela Storz

    (Eunice Kennedy Shriver National Institute of Child Health and Human Development)

  • Kai Papenfort

    (Friedrich Schiller University Jena, Institute of Microbiology
    Friedrich Schiller University Jena)

Abstract

Small regulatory RNAs (sRNAs) acting in concert with the RNA chaperone Hfq are prevalent in many bacteria and typically act by base-pairing with multiple target transcripts. In the human pathogen Vibrio cholerae, sRNAs play roles in various processes including antibiotic tolerance, competence, and quorum sensing (QS). Here, we use RIL-seq (RNA-interaction-by-ligation-and-sequencing) to identify Hfq-interacting sRNAs and their targets in V. cholerae. We find hundreds of sRNA-mRNA interactions, as well as RNA duplexes formed between two sRNA regulators. Further analysis of these duplexes identifies an RNA sponge, termed QrrX, that base-pairs with and inactivates the Qrr1-4 sRNAs, which are known to modulate the QS pathway. Transcription of qrrX is activated by QrrT, a previously uncharacterized LysR-type transcriptional regulator. Our results indicate that QrrX and QrrT are required for rapid conversion from individual to community behaviours in V. cholerae.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35261-x
    DOI: 10.1038/s41467-022-35261-x
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    References listed on IDEAS

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    1. Nikolai Peschek & Roman Herzog & Praveen K. Singh & Marcel Sprenger & Fabian Meyer & Kathrin S. Fröhlich & Luise Schröger & Marc Bramkamp & Knut Drescher & Kai Papenfort, 2020. "RNA-mediated control of cell shape modulates antibiotic resistance in Vibrio cholerae," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    2. Marvin Whiteley & Stephen P. Diggle & E. Peter Greenberg, 2017. "Progress in and promise of bacterial quorum sensing research," Nature, Nature, vol. 551(7680), pages 313-320, November.
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    Cited by:

    1. Fang Liu & Ziying Chen & Shuo Zhang & Kejing Wu & Cheng Bei & Chuan Wang & Yanjie Chao, 2023. "In vivo RNA interactome profiling reveals 3’UTR-processed small RNA targeting a central regulatory hub," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    2. Kejing Wu & Xingyu Lin & Yujie Lu & Rui Dong & Hongnian Jiang & Sarah L. Svensson & Jiajia Zheng & Ning Shen & Andrew Camilli & Yanjie Chao, 2024. "RNA interactome of hypervirulent Klebsiella pneumoniae reveals a small RNA inhibitor of capsular mucoviscosity and virulence," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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