Hfq-licensed RNA-RNA interactome in

Area of Science:

• Bacteriology
• RNA Biology
• Gene Regulation

Background:

• The RNA chaperone Hfq is crucial for bacterial gene regulation by mediating RNA-RNA interactions.
• Pseudomonas aeruginosa possesses numerous small RNAs (sRNAs), but their mRNA targets and functions are largely uncharacterized.
• Understanding sRNA-target interactions is key to deciphering regulatory networks in bacteria.

Purpose of the Study:

• To identify mRNA targets of sRNAs in Pseudomonas aeruginosa using Hfq-dependent RNA-RNA interaction sequencing (RIL-seq).
• To investigate the regulatory mechanisms of the sRNA PhrS, previously thought to target only one mRNA.
• To elucidate the role of PhrS in the synthesis of the quorum sensing signal PQS.

Main Methods:

• Utilized RIL-seq (RNA-chaperone-dependent Interaction and deep Sequencing) in Pseudomonas aeruginosa to map RNA-RNA interactions.
• Bioinformatic analysis to identify sRNA-mRNA pairings mediated by Hfq.
• Experimental validation of PhrS-mRNA interactions and their functional consequences on gene expression.

Main Results:

• Identified mRNA targets for numerous known and novel sRNAs in P. aeruginosa.
• Discovered extensive RNA-RNA interactions involving the sRNA PhrS, revealing it targets hundreds of transcripts.
• Demonstrated that PhrS employs a two-tiered regulatory mechanism for PQS synthesis, controlling both MvfR and AntR transcription regulators.

Conclusions:

• PhrS acts as a keystone sRNA in P. aeruginosa, regulating a broad spectrum of transcripts through direct base-pairing.
• The study reveals a complex, two-tiered regulatory pathway for PQS synthesis governed by PhrS.
• Findings expand the known targets of sRNAs and highlight PhrS as a master regulator in this opportunistic pathogen.