Hfq-licensed RNA-RNA interactome in Pseudomonas aeruginosa reveals a keystone sRNA

Michael J. Gebhardt*, Elizabeth A. Farland, Pallabi Basu, Keven Macareno, Sahar Melamed, Simon L. Dove*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

The RNA chaperone Hfq plays important regulatory roles in many bacteria by facilitating the base pairing between small RNAs (sRNAs) and their cognate mRNA targets. In the gram-negative opportunistic pathogen Pseudomonas aeruginosa, over a hundred putative sRNAs have been identified but for most, their regulatory targets remained unknown. Using RIL-seq with Hfq in P. aeruginosa, we identified the mRNA targets for dozens of previously known and unknown sRNAs. Strikingly, hundreds of the RNA- RNA interactions we discovered involved PhrS. This sRNA was thought to mediate its effects by pairing with a single target mRNA and regulating the abundance of the transcription regulator MvfR required for the synthesis of the quorum sensing signal PQS. We present evidence that PhrS controls many transcripts by pairing with them directly and employs a two-tiered mechanism for governing PQS synthesis that involves control of an additional transcription regulator called AntR. Our findings in P. aeruginosa expand the repertoire of targets for previously known sRNAs, reveal potential regulatory targets for previously unknown sRNAs, and suggest that PhrS may be a keystone sRNA with the ability to pair with an unusually large number of transcripts in this organism.

Original languageAmerican English
Article numbere2218407120
JournalProceedings of the National Academy of Sciences of the United States of America
Volume120
Issue number21
DOIs
StatePublished - 23 May 2023

Bibliographical note

Publisher Copyright:
Copyright © 2023 the Author(s).

Keywords

  • Hfq
  • PhrS
  • posttranscriptional regulator
  • small RNA

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