The alpha subunit of E-coli RNA polymerase activates RNA binding by NusA

The Escherichia coli NusA protein modulates pausing, termination, and antit ermination by associating with the transcribing RNA polymerase core enzyme. NusA can be covalently cross-linked to nascent RNA within a transcription complex, but does not bind RNA on its own. We have found that deletion of t he 79 carboxy-terminal amino acids of the 495-amino-acid NusA protein allow s NusA to bind RNA in gel mobility shift assays. The carboxy-terminal domai n (CTD) of the alpha subunit of RNA polymerase, as well as the bacteriophag e lambda N gene antiterminator protein, bind to carboxy-terminal regions of NusA and enable full-length NusA to bind RNA. Binding of NusA to RNA in th e presence of alpha or N involves an amino-terminal S1 homology region that is otherwise inactive in full-length NusA. The interaction of the alpha -C TD with full-length NusA stimulates termination. N may prevent termination by inducing NusA to interact with N utilization (nut) site RNA rather than RNA near the 3' end of the nascent transcript. Sequence analysis showed tha t the alpha -CTD contains a modified helix-hairpin-helix motif (HhH), which is also conserved in the carboxy-terminal regions of some eubacterial NusA proteins. These HhH motifs may mediate protein-protein interactions in Nus A and the alpha -CTD.