## 2 Gre Factors  
GreA and GreB are transcript cleavage factors that act on backtracked elongation complexes [11, 12, 30]. Backtracking is a phenomenon when RNAP slides backwards along the DNA and the 3' end of the newly synthesised RNA leaves its active center (Figure 1C). While the general structure of the elongation complex (the transcription bubble, the RNA-DNA hybrid) remains unchanged during backtracking, extension of RNA becomes impossible in this conformation. However, such complexes can be resolved by the hydrolytic activity of RNAP, which cleaves the phosphodieser bond in the active center of the backtracked complex, producing a new RNA 3' end in the active center [21, 35]. In the absence of a Gre factor, this hydrolytic reaction is catalyzed by a flexible domain located in the secondary channel called the Trigger Loop (TL; Figure 1C) and the two metal ions of the active center [36]. However, when bound in the secondary channel, Gre factors displace the TL from the active center [37] (Figure 1C). The displacement switches off the relatively slow TL-dependent intrinsic transcript hydrolysis, and imposes the highly efficient Gre-assisted hydrolysis. This efficiency is thought to be due to stabilisation of the second catalytic Mg\({}^{2+}\) ion and an attacking water molecule by the Gre factors [37, 38, 39]. Notably, _E. coli_ GreA has been observed in at least two conformations [33], possibly similar to those of Gfh1, which may be linked to the regulation of transcript hydrolysis (see below). Backtracking may take place after a brief pause in transcription, caused by the thermodynamic properties of nucleic acids sequences surrounding the elongation complex [40]. In addition, misincorporation events render elongation complexes prone to backtracking by at least one bp [41, 42]. In this case, the rescue from backtracking through the cleavage of the 3' end of the erroneous transcript also may be seen as a proofreading reaction. Any backtracking event causes a pause or arrest of transcription elongation, which may limit its overall rate (the average speed of RNAP along the template) or processivity (the fraction of RNAP molecules reaching the end of the gene). Accordingly, Gre factors have been shown _in vitro_ to be general anti-arrest/fidelity factors [12, 41, 42]. However, the roles of Gre factors _in vivo_ in the model bacterium _E. coli_ have been non-trivial to investigate, in part due to their redundancy with additional SCBFs (see below). _E. coli_ Gre factors (GreA and GreB) appear to be not essential, possibly due to their redundancy with DksA (see below), and both can be deleted without seriously affecting cell viability [20, 31]. GreB deletion has been demonstrated to have no phenotype [31]. On the background of GreB deletion, the expression levels of only a few genes were observed to change upon either GreA overproduction (105 genes were activated) or GreA deletion (19 genes were downregulated) [31]. _In vitro_, the presence of GreA decreased the fraction of abortive products from the promoters it was found to activate _in vivo_. Consequently, it was proposed that the main cellular function of GreA is to stimulate escape into productive elongation [31]. Some insights into the Gre factors' _in vivo_ functions were obtained through investigation of the GreA factor from _S. pneumoniae_. This species has a relatively small genome and encodes this single SCBF. The absence of other SCBFs makes this bacterium an ideal model with which to study the function of GreA _in vivo_. In contrast to _E. coli_, deletion of GreA in _S. pneumoniae_ produced a very severe phenotype--cell growth slowed down significantly, and lysis ensued [24]. Despite the pressure on survival, no mutations that would compensate for the loss of GreA, or ease the growth defects were found. Additionally, in contrast to _E. coli_, deletion of GreA downregulated the transcription of approximately 12.5% of the _S.