## 2 Structural Organisation of \(\sigma^{70}\) and Other Group 1 \(\sigma\) Factors
Domain \(\sigma_{4}\) (\(\sigma\)R4.1-4.2) is comprised of four helices with the third and fourth forming a helix-turn-helix motif that binds to the \(-35\) element (Figure 1). Domain \(\sigma_{4}\) forms the second largest interface with RNAP through its interaction with the \(\beta\) flap, and also acts as a contact point for transcriptional activators that bind DNA upstream of \(-35\). A conserved linker (\(\sigma\)R3.2) between \(\sigma_{3}\) and \(\sigma_{4}\) threads through the RNAP active site channel and occupies the RNA exit path, emerging from under the \(\beta\) flap (Figure 1b). Part of the linker, termed the \"\(\sigma\) finger\", facilitates transcription initiation by interacting directly with the template strand, but needs to be displaced when \(>\)4 nt RNA have been synthesized [18] (Figure 1b). Domain \(\sigma_{1.1}\) (\(\sigma\)R.1.1) is only found in Group 1 and promotes a compact form of free \(\sigma\), occluding the DNA binding determinants, and thereby inhibiting its non-productive interaction with promoter DNA in the absence of core [13, 25]. However, upon holoenzyme formation, the negatively-charged \(\sigma_{1.1}\) acts as a DNA mimic, occupying the RNAP active site channel at a position that will subsequently be occupied by duplex DNA in RP\({}_{\text{o}}\)[16, 26, 27]. \(\sigma_{1.1}\) therefore needs to be displaced during RP\({}_{\text{o}}\) formation, such that it acts as a \"gatekeeper\" that stimulates isomerisation at some promoters while inhibiting the process at others [28, 29]. Some Group 1 \(\sigma\) factors additionally contain a non-conserved region (NCR) between \(\sigma\)R1.2 and \(\sigma\)R2.1 that is of variable length and  
Figure 2: Interactions of _E. coli_\(\sigma^{70}\) and \(\sigma^{\text{E}}\) with “flipped out” bases in non-template strand of \(-10\) regions. The \(\sigma^{70}\)-DNA model is a partial representation of a crystal structure of an _E. coli_\(\sigma^{70}\) transcription initiation complex (PDB: 4 YLN) [22] showing the \(\sigma^{70}\)\({}_{2}\) domain interactions with the non-template strand (C\({}_{\text{-13}}\)T\({}_{\text{-12}}\)A\({}_{\text{-11}}\)T\({}_{\text{-10}}\)A\({}_{\text{-9}}\)A\({}_{\text{-8}}\)T\({}_{\text{-7}}\)G\({}_{\text{-6}}\)T\({}_{\text{-5}}\)G-4) Flipped out bases in the \(-10\) element (\(-11\)A and \(-7\)T) and the discriminator element (\(-6\)G) are indicated. Note that DNA upstream of \(-11\)A is double stranded, with the template strand not shown for clarity. The \(\sigma^{\text{E}}\)-DNA model is based on a crystal structure of the _E. coli_\(\sigma^{\text{E}}\)\({}_{2}\) domain bound to a non-template strand oligonucleotide (PDB: 4 LUP) [23] based on the \(\sigma^{\text{E}}\) consensus \(-10\) sequence (T\({}_{\text{-13}}\)G\({}_{\text{-12}}\)T\({}_{\text{-11}}\)C\({}_{\text{-10}}\)A\({}_{\text{-9}}\)A\({}_{\text{-8}}\)A\({}_{\text{-7}}\)). The modular loop that interacts with the flipped out \(-10\)C is indicated. \(\sigma_{2}\) domains are illustrated in surface representation with conserved regions colored as indicated and the \(\sigma^{70}\) NCR not shown. composition and has been implicated in core binding and promoter escape in the case of _E. coli_\(\sigma^{70}\)[30] (Figure 1).