An Atlas of Hfq-bound Transcripts Reveals 3' UTRs as a Genomic Reservoir of Regulatory Small RNAs

EMBO J. 2012 Oct 17;31(20):4005-19. doi: 10.1038/emboj.2012.229. Epub 2012 Aug 24.


The small RNAs associated with the protein Hfq constitute one of the largest classes of post-transcriptional regulators known to date. Most previously investigated members of this class are encoded by conserved free-standing genes. Here, deep sequencing of Hfq-bound transcripts from multiple stages of growth of Salmonella typhimurium revealed a plethora of new small RNA species from within mRNA loci, including DapZ, which overlaps with the 3' region of the biosynthetic gene, dapB. Synthesis of the DapZ small RNA is independent of DapB protein synthesis, and is controlled by HilD, the master regulator of Salmonella invasion genes. DapZ carries a short G/U-rich domain similar to that of the globally acting GcvB small RNA, and uses GcvB-like seed pairing to repress translation of the major ABC transporters, DppA and OppA. This exemplifies double functional output from an mRNA locus by the production of both a protein and an Hfq-dependent trans-acting RNA. Our atlas of Hfq targets suggests that the 3' regions of mRNA genes constitute a rich reservoir that provides the Hfq network with new regulatory small RNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / genetics*
  • Bacterial Proteins / biosynthesis
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Bacterial Proteins / physiology
  • Base Sequence
  • Carrier Proteins / biosynthesis
  • Carrier Proteins / genetics
  • Gene Expression Regulation, Bacterial / genetics*
  • Genes, Bacterial
  • Genes, Overlapping
  • Host Factor 1 Protein / metabolism*
  • Immunoprecipitation
  • Lipoproteins / biosynthesis
  • Lipoproteins / genetics
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Biosynthesis
  • Protein Structure, Tertiary
  • RNA Processing, Post-Transcriptional / genetics*
  • RNA, Bacterial / genetics*
  • RNA, Bacterial / metabolism
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • RNA, Small Untranslated / genetics*
  • Salmonella typhimurium / genetics*
  • Salmonella typhimurium / growth & development
  • Salmonella typhimurium / metabolism
  • Salmonella typhimurium / pathogenicity
  • Sequence Alignment
  • Sequence Analysis, RNA
  • Sequence Homology, Amino Acid
  • Transcription Factors / physiology*
  • Transcription, Genetic
  • Virulence / genetics


  • 3' Untranslated Regions
  • Bacterial Proteins
  • Carrier Proteins
  • HilD protein, Salmonella typhimurium
  • Host Factor 1 Protein
  • Lipoproteins
  • RNA, Bacterial
  • RNA, Messenger
  • RNA, Small Untranslated
  • Transcription Factors
  • oligopeptide-binding protein, bacteria