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

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 sigma(F) to create a negative feedback loop that inhibits sigma(F)-directed gene transcription. Cells deleted for fin are defective for spore formation and exhibit increased levels of sigma(F)-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 subunit. The coiled-coil is a docking site for sigma factors on RNA polymerase, and evidence is presented that the binding of Fin and sigma(F) to RNA polymerase is mutually exclusive. We propose that Fin functions by a mechanism distinct from that of classic sigma factor antagonists (anti-sigma factors), which bind directly to a target sigma factor to prevent its association with RNA polymerase, and instead functions to inhibit sigma(F) by competing for binding to the coiled-coil.