NusA Interaction with the α Subunit of E-coli RNA Polymerase Is via the UP Element Site and Releases Autoinhibition

Elongating Escherichia coli RNAP is modulated by NusA protein. The C-terminal domain (CTD) of the RNAP alpha subunit (alpha CTD) interacts with the acidic CTD 2 (AR2) of NusA, releasing the autoinhibitory blockade of the NusA S1-KH1-KH2 motif and allowing NusA to bind nascent nut spacer RNA. We determined the solution conformation of the AR2:alpha CTD complex. The alpha CTD residues that interface with AR2 are identical to those that recognize UP promoter elements A nusA-Delta AR2 mutation does not affect UP-dependent rrnH transcription initiation in vivo. Instead, the mutation inhibits Rho-dependent transcription termination at phage gamma tR1, which lies adjacent to the gamma nutR sequence. The Rho-dependent gamma timm terminator, which is not preceded by a nut sequence, is fully functional. We propose that constitutive binding of NusA-Delta AR2 to gamma nutR occludes Rho. In addition, the mutation confers a dominant defect in exiting stationary phase.