CBR antimicrobials alter coupling between the bridge helix and the β subunit in RNA polymerase

: Malinen AM, Nandymazumdar M, Turtola M, Malmi H, Grocholski T, Artsimovitch I, Belogurov GA.

: 2014

: Nature Communications

: 3408

: 5

: 9

: 2041-1723

DOI: https://doi.org/10.1038/ncomms4408

: http://www.nature.com/ncomms/2014/140306/ncomms4408/full/ncomms4408.html

Bacterial RNA polymerase (RNAP) is a validated target for antibacterial drugs. CBR703 series antimicrobials allosterically inhibit transcription by binding to a conserved α helix (β′ bridge helix, BH) that interconnects the two largest RNAP subunits. Here we show that disruption of the BH-β subunit contacts by amino-acid substitutions invariably results in accelerated catalysis, slowed-down forward translocation and insensitivity to regulatory pauses. CBR703 partially reverses these effects in CBR-resistant RNAPs while inhibiting catalysis and promoting pausing in CBR-sensitive RNAPs. The differential response of variant RNAPs to CBR703 suggests that the inhibitor binds in a cavity walled by the BH, the β′ F-loop and the β fork loop. Collectively, our data are consistent with a model in which the β subunit fine tunes RNAP elongation activities by altering the BH conformation, whereas CBRs deregulate transcription by increasing coupling between the BH and the β subunit.