A dual reporter system for detecting RNA interactions in bacterial cells

Chembiochem. 2014 Dec 15;15(18):2703-9. doi: 10.1002/cbic.201402322. Epub 2014 Oct 30.


Detecting RNA-partner interactions in cells is often difficult due to a lack of suitable tools. Here we describe a dual reporter system capable of detecting intracellular interactions in which one of the partners is an RNA. The system utilizes two fluorescent proteins with similar maturation rates but distinct spectral properties, specifically cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). By placing the CFP gene upstream and the YFP gene downstream of an RNA gene of interest, the production of YFP becomes sensitive to RNA-partner interaction, whereas the synthesis of CFP is not disturbed. Therefore, the RNA-partner interaction can be simply measured by the change in the ratio of fluorescence of YFP over CFP. The utility of our approach is demonstrated through verification of three known RNA-partner interactions in the model bacterium Escherichia coli. Our two-reporter strategy should be broadly useful to the study of RNA-targeted interactions in bacteria.

Keywords: GcvB; GlmZ; RNA; fluorescent proteins; small RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / analysis
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Base Sequence
  • Cloning, Molecular
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / metabolism
  • Fluorescent Dyes / analysis
  • Fluorescent Dyes / metabolism*
  • Green Fluorescent Proteins / analysis
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism*
  • Luminescent Proteins / analysis
  • Luminescent Proteins / genetics
  • Luminescent Proteins / metabolism*
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism*
  • Spectrometry, Fluorescence


  • Bacterial Proteins
  • Cyan Fluorescent Protein
  • Escherichia coli Proteins
  • Fluorescent Dyes
  • Luminescent Proteins
  • RNA, Bacterial
  • yellow fluorescent protein, Bacteria
  • Green Fluorescent Proteins