The α subunit of E. coli RNA polymerase activates RNA binding by NusA

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Abstract
The Escherichia coli NusA protein modulates pausing, termination, and antitermination 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 the 79 carboxy-terminal amino acids of the 495-amino-acid NusA protein allows NusA to bind RNA in gel mobility shift assays. The carboxy-terminal domain (CTD) of the α subunit of RNA polymerase, as well as the bacteriophage λ Ngene antiterminator protein, bind to carboxy-terminal regions of NusA and enable full-length NusA to bind RNA. Binding of NusA to RNA in the presence of α or N involves an amino-terminal S1 homology region that is otherwise inactive in full-length NusA. The interaction of the α-CTD 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 that the α-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 NusA and the α-CTD.