Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Ruben A T Mars, Pierre Nicolas, Emma L Denham, Jan Maarten van Dijl

Research output: Contribution to journalReview article

15 Citations (Scopus)

Abstract

Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans-acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5' untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella. Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis. A recent study identified 1,583 putative regulatory RNAs in B. subtilis, whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis, and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5' ends of mRNA molecules. These can include 5' secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis. Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis.

Original languageEnglish
Pages (from-to)1029-1057
Number of pages29
JournalMicrobiology and molecular biology reviews : MMBR
Volume80
Issue number4
DOIs
Publication statusPublished - 26 Oct 2016

Keywords

  • 3' Untranslated Regions/genetics
  • 5' Untranslated Regions/genetics
  • Bacillus subtilis/genetics
  • Gene Expression Regulation, Bacterial/genetics
  • RNA, Antisense/genetics
  • RNA, Bacterial/genetics
  • RNA, Small Untranslated/genetics
  • RNA, Transfer/genetics
  • Regulatory Sequences, Ribonucleic Acid/genetics
  • Riboswitch/genetics

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