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

Michaela Huber, Anne Lippegaus, Sahar Melamed, Malte Siemers, Benjamin R. Wucher, Mona Hoyos, Carey Nadell, Gisela Storz and Kai Papenfort ()
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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
Malte Siemers: Friedrich Schiller University Jena, Institute of Microbiology
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

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-35261-x

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