Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA

Genes Dev. 2005 Oct 1;19(19):2355-66. doi: 10.1101/gad.354405.


This paper shows that the small RNA MicA (previously SraD) is an antisense regulator of ompA in Escherichia coli. MicA accumulates upon entry into stationary phase and down-regulates the level of ompA mRNA. Regulation of ompA (outer membrane protein A), previously attributed to Hfq/mRNA binding, is lost upon deletion of the micA gene, whereas overexpression of MicA inhibits the synthesis of OmpA. In vitro, MicA binds to the ompA mRNA leader. Enzymatic and chemical probing was used to map the structures of MicA, the ompA mRNA leader, and the complex formed upon binding. MicA binding generates a footprint across the ompA Shine-Dalgarno sequence, consistent with a 12 + 4 base-pair interaction, which is additionally supported by the effect of mutations in vivo and by bioinformatics analysis of enterobacterial micA/ompA homolog sequences. MicA is conserved in many enterobacteria, as is its ompA target site. In vitro toeprinting confirmed that binding of MicA specifically interferes with ribosome binding. We propose that MicA, when present at high levels, blocks ribosome binding at the ompA translation start site, which-in line with previous work-secondarily facilitates RNase E cleavage and subsequent mRNA decay. MicA requires the presence of the Hfq protein, although the mechanistic basis for this remains unclear.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Outer Membrane Proteins / biosynthesis*
  • Bacterial Outer Membrane Proteins / genetics
  • Codon, Initiator / genetics
  • Codon, Initiator / metabolism
  • Endoribonucleases / metabolism
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / biosynthesis*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Gene Deletion
  • Gene Expression Regulation, Bacterial / genetics*
  • Host Factor 1 Protein / genetics
  • Host Factor 1 Protein / metabolism*
  • Protein Biosynthesis / genetics
  • RNA Interference / physiology
  • RNA Stability / genetics
  • RNA, Antisense / genetics
  • RNA, Antisense / metabolism*
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism*
  • Regulatory Sequences, Ribonucleic Acid / physiology
  • Ribosomes / metabolism


  • Bacterial Outer Membrane Proteins
  • Codon, Initiator
  • Escherichia coli Proteins
  • Hfq protein, E coli
  • Host Factor 1 Protein
  • RNA, Antisense
  • RNA, Bacterial
  • Regulatory Sequences, Ribonucleic Acid
  • OMPA outer membrane proteins
  • Endoribonucleases
  • ribonuclease E