A novel RNA polymerase-binding protein that interacts with a sigma-factor docking site

Mol Microbiol. 2017 Aug;105(4):652-662. doi: 10.1111/mmi.13724. Epub 2017 Jun 19.


Sporulation in Bacillus subtilis is governed by a cascade of alternative RNA polymerase sigma factors. We previously identified a small protein Fin that is produced under the control of the sporulation sigma factor σF to create a negative feedback loop that inhibits σF -directed gene transcription. Cells deleted for fin are defective for spore formation and exhibit increased levels of σF -directed gene transcription. Based on pull-down experiments, chemical crosslinking, bacterial two-hybrid experiments and nuclear magnetic resonance chemical shift analysis, we now report that Fin binds to RNA polymerase and specifically to the coiled-coil region of the β' subunit. The coiled-coil is a docking site for sigma factors on RNA polymerase, and evidence is presented that the binding of Fin and σF to RNA polymerase is mutually exclusive. We propose that Fin functions by a mechanism distinct from that of classic sigma factor antagonists (anti-σ factors), which bind directly to a target sigma factor to prevent its association with RNA polymerase, and instead functions to inhibit σF by competing for binding to the β' coiled-coil.

MeSH terms

  • Bacillus subtilis / genetics
  • Bacillus subtilis / metabolism
  • Bacterial Proteins / metabolism
  • DNA-Directed RNA Polymerases / metabolism*
  • DNA-Directed RNA Polymerases / physiology*
  • Gene Expression Regulation, Bacterial / genetics
  • Protein Binding / physiology
  • Protein Structure, Tertiary
  • RNA-Binding Proteins / metabolism
  • Sigma Factor / metabolism
  • Sigma Factor / physiology*
  • Spores, Bacterial / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic / genetics


  • Bacterial Proteins
  • RNA-Binding Proteins
  • Sigma Factor
  • Transcription Factors
  • DNA-Directed RNA Polymerases