Identification of regulatory RNAs in Bacillus subtilis

Nucleic Acids Res. 2010 Oct;38(19):6637-51. doi: 10.1093/nar/gkq454. Epub 2010 Jun 4.


Post-transcriptional regulatory mechanisms are widespread in bacteria. Interestingly, current published data hint that some of these mechanisms may be non-random with respect to their phylogenetic distribution. Although small, trans-acting regulatory RNAs commonly occur in bacterial genomes, they have been better characterized in Gram-negative bacteria, leaving the impression that they may be less important for Firmicutes. It has been presumed that Gram-positive bacteria, in particular the Firmicutes, are likely to utilize cis-acting regulatory RNAs located within the 5' mRNA leader region more often than trans-acting regulatory RNAs. In this analysis we catalog, by a deep sequencing-based approach, both classes of regulatory RNA candidates for Bacillus subtilis, the model microorganism for Firmicutes. We successfully recover most of the known small RNA regulators while also identifying a greater number of new candidate RNAs. We anticipate these data to be a broadly useful resource for analysis of post-transcriptional regulatory strategies in B. subtilis and other Firmicutes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions
  • Bacillus subtilis / genetics*
  • Bacterial Toxins / genetics
  • Base Sequence
  • Molecular Sequence Data
  • Prophages / genetics
  • RNA, Antisense / analysis
  • RNA, Bacterial / analysis
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / genetics
  • RNA, Small Untranslated / analysis*
  • RNA, Small Untranslated / chemistry
  • RNA, Small Untranslated / genetics
  • Sequence Analysis, RNA


  • 5' Untranslated Regions
  • Bacterial Toxins
  • RNA, Antisense
  • RNA, Bacterial
  • RNA, Small Untranslated