## 5 NusG, NusA and DksA
### DksA  
DksA was originally isolated as a suppressor of a chaperone mutation, _dnaK_. It was then shown to disrupt RNAP open complexes at _rrn_ promoters under the influence of ppGpp and NTP [65]. DksA and GreA/B belong to a family of coiled-coil proteins that bind within the secondary channel of RNAP. Despite structural similarities to GreA/B, DksA cannot induce RNAP to cleave RNA in backtracked RNAP.  
The critical difference between DksA and GreA/B lies in a few residues at the tip of the coiled coil. These residues contact the RNAP active center [66]. There is physiological interplay between the two functions. Thus, microarray analysis indicates that many genes are similarly regulated by DksA and GreA. GreA overproduction can suppress a _dksA_ growth defect. At other genetic loci, however, DksA and GreA act oppositely. The biochemical basis of these interactions remains to be elucidated [67]. Like DksA, GreA can act at promoters, where it facilitates promoter escape. In particular, this activity of GreA strongly stimulates expression of ribosomal protein operons and the _tna_ operon [68].  
The fact that ppGpp inhibits RNA chain extension prompted experiments to test if DksA also acted on TEC _in vitro_. Although wild-type DksA has little or no effect on the rate of RNA synthesis with wild-type RNAP, a DksA mutant with enhanced affinity for RNAP slows elongation in a ppGpp-independent fashion, although this effect is stimulated by ppGpp. Similarly, wild-type DksA retards RNA synthesis by an RNAP mutant with increased sensitivity to DksA, again independently of ppGpp. The template used in these studies lacked paused sites, suggesting that DksA does not slow transcription elongation by stimulating pausing. Finally, DksA stimulates termination at the intrinsic _rrnB_ T1 terminator [69].  
_In vivo_, mutational studies implicate DksA in preventing transcription-replication conflicts. DksA protects cells against UV and other DNA damage, which inhibit transcription elongation [70]. DksA prevents replication arrest in amino acid-starved cells via effects on transcription elongation [71]. Amino acid starvation, which stalls translation, arrests DNA replication in the absence of DksA [71]. This is consistent with the idea that TEC can uncouple from stalled ribosomes and, if not removed by Rho, will backtrack and form a barrier to replication [39; 64]. [PERSON] _et al._[71] propose that DksA prevents backtracking of uncoupled TEC (rather than resolving backtracked TEC), and, therefore, suppresses replisome clashes. The mechanism by which DksA might accomplish this reaction remains undefined.  
A genome wide survey of TEC occupancy in the presence or absence of DksA supports the notion that DksA suppresses replisome clashes by acting on backtracked TEC. ChIP-chip experiments reveal that DksA is enriched both at promoters and in downstream regions, colocalizing with RNAP across the entire chromosome. DksA suppresses TEC stalling induced by amino acid starvation globally, possibly by blocking backtracking [72]. An alternate interpretation, that DksA removes uncoupled TEC ahead of the replisome, suggested by _in vitro_ studies, has not been ruled out [69]. Genetic evidence further complicates the picture. Thus the sensitivity of _dksA_ mutants to the DNA cross-linker, mitomycin C, is suppressed by a second mutation in _greA_[73]. Since both mutations are proposed to increase backtracking or stabilize the backtracked TEC, it is difficult to rationalize this suppression pattern. Reconciling these _in vitro_ and _in vivo_ observations will be, we are afraid, the task of future generations.