The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress in E. coli

RNA Biol. 2012 Apr;9(4):458-68. doi: 10.4161/rna.19065. Epub 2012 Feb 16.


In bacteria, adaptive response to external stimuli is often regulated by small RNAs (sRNAs). In Escherichia coli, the organism in which sRNAs have been best characterized so far, no function could be attributed to 40 out of 79 sRNAs. Here we decipher the function of RybA, one of these orphan sRNAs. RybA was discovered in 2001 by Wassarman et al. using comparative genomics. This sRNA is conserved between E. coli, Salmonella typhimurium and Klebsiella pneumoniae. We determined the expression pattern of RybA under different growth conditions and identified its exact 5' and 3' ends. Using microarray and Northern analysis we show that, under peroxide stress, the absence of RybA leads to an upregulation of key genes of the TyrR regulon involved in the metabolism of aromatic compounds including the aromatic amino acids. Although containing an open reading frame, which might have an independent function, RybA does not require translation for this activity and therefore acts at the RNA level. Furthermore we demonstrate that regulation requires the transcription regulator TyrR. The mechanism of activation of TyrR, probably the primary target of RybA, remains to be elucidated. The downregulation of aromatic amino acid biosynthesis might regulate the cellular concentration of chorismate and its availability for other downstream products like ubiquinone or enterobactin. While ubiquinone participates in the defense against oxidative stress in the cytoplasmic membrane, enterobactin is involved in iron import and is therefore detrimental under oxidative stress.

MeSH terms

  • Amino Acids, Aromatic / biosynthesis*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Escherichia coli / physiology
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Gene Expression Regulation, Bacterial
  • Gene Knockout Techniques
  • Genes, Bacterial
  • Hydrogen Peroxide / pharmacology*
  • Oligonucleotide Array Sequence Analysis
  • Oxidants / pharmacology*
  • RNA, Bacterial / genetics*
  • RNA, Bacterial / physiology
  • RNA, Small Untranslated / genetics*
  • RNA, Small Untranslated / physiology
  • Sequence Analysis, DNA
  • Stress, Physiological / genetics
  • Transcriptome


  • Amino Acids, Aromatic
  • Escherichia coli Proteins
  • Oxidants
  • RNA, Bacterial
  • RNA, Small Untranslated
  • Hydrogen Peroxide