Natural RNA Polymerase Aptamers Regulate Transcription in E. coli

Mol Cell. 2017 Jul 6;67(1):30-43.e6. doi: 10.1016/j.molcel.2017.05.025. Epub 2017 Jun 22.


In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP), we deep sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches, we characterized a subset of inhibitory RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing environment. The mechanism of iRAPs involves active uncoupling of transcription and translation, making nascent RNA accessible to Rho. iRAPs encoded in the antisense strand also promote gene expression by reducing transcriptional interference. In essence, our work uncovers a broad class of cis-acting RNA signals that globally control bacterial transcription.

Keywords: aptamers; regulatory RNA; termination; transcription elongation.

MeSH terms

  • Aptamers, Nucleotide / genetics*
  • Aptamers, Nucleotide / metabolism
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • DNA-Directed RNA Polymerases / genetics*
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli / enzymology
  • Escherichia coli / genetics*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial
  • Nicotinamide-Nucleotide Adenylyltransferase / genetics
  • Nicotinamide-Nucleotide Adenylyltransferase / metabolism
  • Open Reading Frames
  • Ribosomes / metabolism
  • SELEX Aptamer Technique*
  • Time Factors
  • Transcription Termination, Genetic*


  • Aptamers, Nucleotide
  • Bacterial Proteins
  • Escherichia coli Proteins
  • Rho protein, E coli
  • Nicotinamide-Nucleotide Adenylyltransferase
  • nicotinic acid mononucleotide adenylyltransferase
  • DNA-Directed RNA Polymerases