Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA

Mol Microbiol. 2012 May;84(3):428-45. doi: 10.1111/j.1365-2958.2012.08031.x. Epub 2012 Mar 28.


MicF is a textbook example of a small regulatory RNA (sRNA) that acts on a trans-encoded target mRNA through imperfect base pairing. Discovery of MicF as a post-transcriptional repressor of the major Escherichia coli porin OmpF established the paradigm for a meanwhile common mechanism of translational inhibition, through antisense sequestration of a ribosome binding site. However, whether MicF regulates additional genes has remained unknown for almost three decades. Here, we have harnessed the new superfolder variant of GFP for reporter-gene fusions to validate newly predicted targets of MicF in Salmonella. We show that the conserved 5' end of MicF acts by seed pairing to repress the mRNAs of global transcriptional regulator Lrp, and periplasmic protein YahO, while a second targeting region is also required to regulate the mRNA of the lipid A-modifying enzyme LpxR. Interestingly, MicF targets lpxR at both the ribosome binding site and deep within the coding sequence. MicF binding in the coding sequence of lpxR decreases mRNA stability through exacerbating the use of a native RNase E site proximal to the short MicF-lpxR duplex. Altogether, this study assigns the classic MicF sRNA to the growing class of Hfq-associated regulators that use diverse mechanisms to impact multiple loci.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Base Pairing
  • Base Sequence
  • Conserved Sequence
  • Gene Expression Regulation, Bacterial*
  • Genes, Reporter
  • Green Fluorescent Proteins / chemistry
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism*
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Porins / genetics*
  • Porins / metabolism
  • Protein Folding
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Small Untranslated / chemistry
  • RNA, Small Untranslated / genetics
  • RNA, Small Untranslated / metabolism*
  • Salmonella typhimurium / chemistry
  • Salmonella typhimurium / genetics
  • Salmonella typhimurium / metabolism*


  • 5' Untranslated Regions
  • Bacterial Proteins
  • Porins
  • RNA, Bacterial
  • RNA, Messenger
  • RNA, Small Untranslated
  • Green Fluorescent Proteins