## 5 NusG, NusA and DksA
### NusG  
The 21 kDa _E. coli_ NusG is composed of two domains connected by a flexible linker. It affects transcription elongation through a variety of mechanisms. The NusG-NTD directly suppresses pausing and thus enhances the overall rate of transcription elongation [49]. Structural studies with the archaeal NusG homologue, Spt5, suggests that the NusG-NTD enhances TEC processivity by completely encircling the DNA binding channel of RNAP, thus stabilizing the closed conformation of the RNAP clamp domain [50]. Single molecule analyses indicate that NusG decreases the rate of entry into both short-lifetime and, more significantly, long-lifetime pauses. Suppression of long-lifetime pauses is proposed to account for NusG-NTD enhancement of transcription elongation. According to this model, NusG-NTD increases movement of TEC along the DNA template by promoting transition from the pre-translocated towards the post-translocated register [51].  
The NusG-CTD KOW domain interacts with NusE/S10, thus linking TEC to the lead ribosome. Coupling of transcription to translation suppresses backtracking and possible clashes with the replisome [45]. The NusG-CTD also binds to--and activates--termination factor Rho with the same interface with which it binds NusE/S10. Thus ribosome-associated NusG-CTD is not available to enhance Rho-dependent termination [52]. Linkage between the lead ribosome and TEC also suppresses formation of untranslated RNA, which is required for Rho to access TEC. Sequestering of the NusG-CTD and the absence of RNA ligand together account for the absence of Rho-dependent termination in well-translated genes.  
_In vivo_, it is not known whether NusG associates first with RNAP, with ribosomes or simultaneously to both. Genome-wide surveys suggest that NusG associates with TEC only after significant elongation has occurred [36]. This is difficult to reconcile with the coupling hypothesis, since free TEC could be targeted by Rho (see below). On the other hand, the _E. coli_ NusG paralogue, RfaH, appears to link ribosomes to TEC early after transcription initiation [53].  
The _in vivo_ calculated/reported numbers for NusG [54] is one sixth the number of ribosomes (\(\approx\)55,000 copies/cell, [55]). This is consistent with the idea that only the first ribosome in translating polysomes associates with NusG and TEC.  
However, ribosomal stalling at rare codons or induced by amino acid analogues can uncouple transcription from translation and induce intragenic Rho-dependent termination. The stalled ribosome is attacked by tmRNA, which competes for binding with NusG-CTD to S10 and releases the impacted ribosome [40].  
Activation of Rho explains why NusG is essential in wild-type _E. coli_. The cryptic _rac_ prophage carries a constitutive promoter and a downstream _kil_ gene whose expression is lethal to the bacterial host. Rho-dependent termination prevents transcription extension from the promoter to _kil_. Deletion of the _rac_ prophage allows _E. coli_ to support a _nusG_ deletion, although the mutant strain grows poorly and dies in stationary phase [38].  
Oddly, _B. subtilis_ NusG stimulates pausing at two regulatory sites in the untranslated leader of the _B. subtilis trp_ operon that participate in transcription attenuation and translational control mechanisms, respectively. To induce pausing, _B. subtilis_ NusG makes sequence-specific contacts with a T-rich sequence in the nontemplate DNA strand within the paused transcription bubble [56]. The _E. coli_ NusG homologue, RfaH, makes similar contacts with the template _ops_ element. Pausing at _ops_ may allow RfaH to link to the lead ribosome and couple transcription to translation in _ops_-bearing operons [57].