Switching fatty acid metabolism by an RNA-controlled feed forward loop

Area of Science:

• Microbiology
• Molecular Biology
• Bacterial Pathogenesis

Background:

• Host factor for phage Q beta (Hfq) is essential for bacterial posttranscriptional gene regulation by stabilizing small RNAs (sRNAs) and mediating their interactions with target mRNAs.
• In the pathogen *Vibrio cholerae*, Hfq loss impacts virulence, biofilm formation, and communication, but its RNA targets remain unidentified.

Purpose of the Study:

• To identify the RNA ligands bound by Hfq in *Vibrio cholerae* using RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq).
• To characterize the function of a novel Hfq-associated sRNA involved in fatty acid metabolism.

Main Methods:

• RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq) was employed to capture and identify RNAs associated with Hfq in *V. cholerae*.
• Bioinformatic analysis was performed to identify Hfq-bound coding and noncoding transcripts.
• Molecular and genetic techniques were used to investigate the function of the identified sRNA, FarS, and its role in fatty acid metabolism.

Main Results:

• RIP-seq identified 603 coding and 85 noncoding transcripts bound by Hfq.
• Forty-four novel sRNAs were discovered, including FarS, derived from the 3' untranslated region (UTR) of the *fabB* mRNA.
• FarS, in conjunction with Hfq, was shown to inhibit the expression of *fadE* mRNAs, forming a regulatory loop with FadR to control fatty acid metabolism.

Conclusions:

• This study provides the first comprehensive identification of Hfq-bound RNAs in *Vibrio cholerae*, establishing a molecular foundation for understanding Hfq-mediated regulation.
• A previously unrecognized sRNA, FarS, plays a critical role in regulating fatty acid biosynthesis and degradation pathways in this major human pathogen.