## 5 NusG, NusA and DksA
### NusA  
_E. coli_ NusA protein was originally identified genetically as a required component of the phage \(\lambda\) N antitermination complex, and biochemically as a factor that stimulated _lacZ_ gene expression _in vitro_[58]. RNAP is modulated by NusA protein and _vice versa_. NusA enhances pausing as well as termination at intrinsic termination sites. Paradoxically, it also suppresses transcription termination as part of the \(\lambda\) N or _rrn_ antitermination complexes. NusA is thought to provoke termination when present in 1:1 stochiometry with RNAP, and antitermination--as part of the NusBEG/\(\lambda\) N complex--when the stoichiometry is 2:1. Numerous studies place NusA near the RNA exit channel [59]. [PERSON] and [PERSON] [60] proposed that NusA weakens RNA binding to the upstream bindings elements (UBS) in the channel, allowing formation of the RNA stem-loop that induces termination at intrinsic terminators. However, direct binding of NusA-NTD to RNA:RNA duplexes in the exit channel has recently been demonstrated [61]. Thus, direct stabilization of RNA:RNA hybrids in the exit channel might instead be responsible for NusA stimulation of pausing and intrinsic termination.  
The NusABEG/\(\lambda\)N antitermination complex forms at the NUT sequences of \(\lambda\) nascent transcript. These sequences lie in the phage chromosome between the \(\lambda\)_pL_ and \(\lambda\)_pR_ promoters and the first termination signals in their operons. NusA binds to the NUT SPACER sequence within NUT. However, NusA binding to RNA is dependent on its association with TEC. NusA binds to TEC via two distinct domains, the NTD and an acidic domain in the CTD (AR2). 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 RNA. The solution conformation of the AR2:\(\alpha\)CTD complex shows that the \(\alpha\)CTD residues that interface with AR2 are identical to those that recognize UP promoter elements. This is consistent with a role for NusA in transcription initiation of operons carrying UP elements, although evidence for such an activity has yet to be unearthed [62].  
Earlier studies suggested that the binding of NusA-NTD and \(\sigma\)70 to RNAP were mutually exclusive. However, recent structural data shows association of NusA-NTD and the \(\beta\)-flap tip helix, a site distinct from that of the major \(\sigma\)70 region 2 binding site, the CH region of the \(\beta\)' subunit. Nevertheless, NusA might compete with the weak binding of \(\sigma\)70 region 4 to the \(\beta\)-flap tip [63].  
Unlike NusG, complete deletions of NusA cannot be constructed. A NusA truncation that retains the NusA-NTD can be introduced into strain MDS42, which lacks all horizontally transmitted elements, including the cryptic _rac_ prophage [64]. This is explained by the finding that the NusA-NTD has biochemical activity; NusA-NTD by itself is necessary and sufficient for enhancement of transcriptional pausing. The other, dispensable, NusA domains provide additional, interactions with TEC and are required to stimulate intrinsic termination [61].