biostudies-literatureWang Erickson AFNational Institutes of HealthWellcome TrustBiotechnology and Biological Sciences Research CouncilNIGMS NIH HHS652-662https://www.ebi.ac.uk/biostudies/studies/S-EPMC5558796biostudies-literatureUnknown105(4)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 σ^F to create a negative feedback loop that inhibits σ^F -directed gene transcription. Cells deleted for fin are defective for spore formation and exhibit increased levels of σ^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 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 σ^F 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 σ^F by competing for binding to the β' coiled-coil.Molecular microbiologyA novel RNA polymerase-binding protein that interacts with a sigma-factor docking site.PMC5558796R01 GM044025GM18658BB/L006952/1 and BB/N006267/1BB/N006267/1BB/R006091/1GM044025BB/L006952/1R01 GM018568Hochschild ABarrasso KKrysztofinska EMIsaacson RLWang Erickson AFAlfano CLosick RDeighan PMartinez-Lumbreras SChen SGarcia CPCamp AHThapaliya AfalseA 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 σ^F to create a negative feedback loop that inhibits σ^F -directed gene transcription. Cells deleted for fin are defective for spore formation and exhibit increased levels of σ^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 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 σ^F 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 σ^F by competing for binding to the β' coiled-coil.2017-01-01T00:00:00Z2017 Aug2024-10-18T04:30:19.223Z2019-03-26T23:48:41ZS-EPMC55587962859801710.1111/mmi.13724