Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli

Mol Cell. 2014 Jul 17;55(2):199-213. doi: 10.1016/j.molcel.2014.05.006. Epub 2014 Jun 5.


In bacteria, Hfq is a core RNA chaperone that catalyzes the interaction of mRNAs with regulatory small RNAs (sRNAs). To determine in vivo RNA sequence requirements for Hfq interactions, and to study riboregulation in a bacterial pathogen, Hfq was UV crosslinked to RNAs in enterohemorrhagic Escherichia coli (EHEC). Hfq bound repeated trinucleotide motifs of A-R-N (A-A/G-any nucleotide) often associated with the Shine-Dalgarno translation initiation sequence in mRNAs. These motifs overlapped or were adjacent to the mRNA sequences bound by sRNAs. In consequence, sRNA-mRNA duplex formation will displace Hfq, promoting recycling. Fifty-five sRNAs were identified within bacteriophage-derived regions of the EHEC genome, including some of the most abundant Hfq-interacting sRNAs. One of these (AgvB) antagonized the function of the core genome regulatory sRNA, GcvB, by mimicking its mRNA substrate sequence. This bacteriophage-encoded "anti-sRNA" provided EHEC with a growth advantage specifically in bovine rectal mucus recovered from its primary colonization site in cattle.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites
  • Cattle
  • Consensus Sequence
  • Escherichia coli O157 / genetics
  • Escherichia coli O157 / metabolism
  • Escherichia coli O157 / virology*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Gene Expression Regulation, Bacterial
  • Heme Oxygenase (Decyclizing) / genetics
  • Heme Oxygenase (Decyclizing) / metabolism
  • Host Factor 1 Protein / metabolism
  • Molecular Sequence Data
  • Mucus / microbiology
  • Prophages / genetics*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Small Untranslated / genetics
  • RNA, Small Untranslated / metabolism*
  • RNA, Viral / genetics*
  • RNA, Viral / metabolism


  • Escherichia coli Proteins
  • Hfq protein, E coli
  • Host Factor 1 Protein
  • RNA, Messenger
  • RNA, Small Untranslated
  • RNA, Viral
  • Heme Oxygenase (Decyclizing)

Associated data

  • GEO/GSE46113
  • GEO/GSE46118
  • GEO/GSE46120