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

Proc Natl Acad Sci U S A. 2020 Apr 7;117(14):8044-8054. doi: 10.1073/pnas.1920753117. Epub 2020 Mar 19.


Hfq (host factor for phage Q beta) is key for posttranscriptional gene regulation in many bacteria. Hfq's function is to stabilize sRNAs and to facilitate base-pairing with trans-encoded target mRNAs. Loss of Hfq typically results in pleiotropic phenotypes, and, in the major human pathogen Vibrio cholerae, Hfq inactivation has been linked to reduced virulence, failure to produce biofilms, and impaired intercellular communication. However, the RNA ligands of Hfq in V. cholerae are currently unknown. Here, we used RIP-seq (RNA immunoprecipitation followed by high-throughput sequencing) analysis to identify Hfq-bound RNAs in V. cholerae Our work revealed 603 coding and 85 noncoding transcripts associated with Hfq, including 44 sRNAs originating from the 3' end of mRNAs. Detailed investigation of one of these latter transcripts, named FarS (fatty acid regulated sRNA), showed that this sRNA is produced by RNase E-mediated maturation of the fabB 3'UTR, and, together with Hfq, inhibits the expression of two paralogous fadE mRNAs. The fabB and fadE genes are antagonistically regulated by the major fatty acid transcription factor, FadR, and we show that, together, FadR, FarS, and FadE constitute a mixed feed-forward loop regulating the transition between fatty acid biosynthesis and degradation in V. cholerae Our results provide the molecular basis for studies on Hfq in V. cholerae and highlight the importance of a previously unrecognized sRNA for fatty acid metabolism in this major human pathogen.

Keywords: RNase E; Vibrio cholerae; fatty acid metabolism; feed-forward loop; small RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / genetics
  • 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase / genetics*
  • Acyl-CoA Dehydrogenase / metabolism
  • Bacterial Proteins / metabolism
  • Fatty Acids / metabolism*
  • Gene Expression Regulation, Bacterial*
  • Host Factor 1 Protein / metabolism
  • RNA Interference
  • RNA, Bacterial / isolation & purification
  • RNA, Small Untranslated / metabolism*
  • Repressor Proteins / metabolism
  • Vibrio cholerae / genetics*
  • Vibrio cholerae / metabolism


  • 3' Untranslated Regions
  • Bacterial Proteins
  • FadR protein, Bacteria
  • Fatty Acids
  • Host Factor 1 Protein
  • RNA, Bacterial
  • RNA, Small Untranslated
  • Repressor Proteins
  • Acyl-CoA Dehydrogenase
  • 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase