## 1 Introduction
Interestingly, the genes coding for secondary channel binding factors are absent from several bacterial genera such as the cyanobacteria and several smaller groups (Aquificaceae, Dictyogolomaceae and Fusobacteriaceae) [25], suggesting that specific features of their RNAPs may compensate for the lack of SCBFs. Figure 1: Secondary channel binding factors (SCBFs). (**A**) Structure of the transcription elongation complex [26] was superimposed with structure of the elongation complex with factor Gfh1 [27]. The RNAP core is represented as a partially transparent grey surface with nucleic acids shown as ribbons and active center Mg\({}^{2+}\) ions as red spheres. Gfh1 bound in the secondary channel is shown as purple ribbons; (**B**) Aligned available structures of bacterial SCBFs. The long N-terminal coiled-coil domain protrudes through the secondary channel of RNAP (see panel B), while the C-terminal globular domain is thought to be responsible for binding to RNAP. Note that the coiled-coil domain of Rnk is shorter than those of the other SCBFs and is turned relative to the C-terminal domain; (**C**) The mode of functioning of Gre factors, and the hypothetical mode of action for other SCBFs. The Gre factor is bound to the active elongation complex but does not impose hydrolytic activity on it [28]. Upon backtracking or misincorporation, the Gre factor protrudes its coiled-coil domain through the secondary channel of RNAP, where it substitutes for the catalytic domain Trigger Loop (TL). This substitution switches off the slow TL-dependent phosphodiester bond hydrolysis and, instead, facilitates highly efficient Gre-dependent hydrolysis. After resolution of the backtracked complex through RNA cleavage, the elongation complex  
returns to the active conformation and the Gre factor gives way to the TL, which can now continue catalysis of RNA synthesis. The controlled switching between Gre and the TL eliminates possible interference of Gre with the RNA synthesis. It is possible that other SCBFs may act in a similar way to that of Gre by substituting the TL in the secondary channel in response to a stimuli (which remain unidentified for other SCBFs). For example, our recent results suggest that DksA may respond to binding of an incorrect NTP in the active center, and thus increase the accuracy of transcription (see text and Figure 2 for details) [29]. \begin{table}
\begin{tabular}{|p{56.9 pt}|p{142.3 pt}|p{142.3 pt}|} \hline \hline
**Group** & **SCBF** & **Function** \\ \hline \hline \multirow{2}{*}{Cleavage factors} & GreA/GreB & Resolve backtracked and misincorporated complexes via phosphodiester bond hydrolysis [11, 30]. Increase clearance from some promoters [31] \\ \cline{2-3}  & DksA+ppGpp & Control isomerisation step of promoter open complexes formation on some promoters [16, 32]. Increases fidelity of transcription elongation [29] \\ \cline{2-3}  & TraR & Encoded on the conjugative plasmid. Acts similarly to DksA on initiation of transcription with no requirement for ppGpp [17] \\ \hline \multirow{2}{*}{Unknown function} & Rnk & Binds RNAP but function is unknown [18] \\ \cline{2-3}  & Gfh1/Rv3788 & Inhibit catalysis by RNAP [33, 34] \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Secondary channel binding factors discussed in this review. Figure 2: Similar roles for Gre and DksA during transcription elongation. Backtracking caused by misincorporation leads to a pause in transcription as with sequence-dependent backtracking, and may lead to the formation of RNAP traffic jams and collisions with replication forks. Gre factors resolve backtracked complexes formed by either mechanism. While DksA cannot prevent or resolve sequence-dependent backtracking, it increases accuracy of RNA synthesis and, thus, reduces the chance of misincorporation and, consequently, reduces formation of one base pair backtracked pause.