Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution

J Mol Evol. 2017 Apr;84(4):204-213. doi: 10.1007/s00239-017-9793-9. Epub 2017 Apr 12.


Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks. Furthermore, it has previously been difficult to trace the evolutionary histories of sRNAs because rapid evolution obscures their original sources. We overcame this challenge by identifying a recently evolved sRNA in Escherichia coli, which allowed us to determine that novel sRNAs could emerge from vestigial bacteriophage genes, the first known source for sRNA origination.

Keywords: Bacteriophage; Non-coding RNA; Small RNA; ncRNA; sRNA evolution.

MeSH terms

  • Bacteria / genetics
  • Base Sequence
  • Biological Evolution
  • Conserved Sequence
  • Enterobacteriaceae / genetics
  • Escherichia coli / genetics*
  • Escherichia coli Proteins / genetics
  • Evolution, Molecular
  • Gene Expression Regulation, Bacterial / genetics
  • Genome, Bacterial / genetics
  • Phylogeny
  • RNA, Bacterial / genetics*
  • RNA, Untranslated / genetics*
  • RNA, Untranslated / metabolism


  • Escherichia coli Proteins
  • RNA, Bacterial
  • RNA, Untranslated