## 2 Structural Organisation of \(\sigma^{70}\) and Other Group 1 \(\sigma\) Factors  
Groups 1 to 4 in the \(\sigma^{70}\) family differ by the presence and absence of four conserved regions (\(\sigma\) Regions \(\sigma\)R1.1, \(\sigma\)R1.2-2.4, \(\sigma\)R3.0-3.2, \(\sigma\)R4.1-4.2; [10,11]) that reflect four helical structured domains (\(\sigma\)1.1, \(\sigma\)2, \(\sigma\)3, \(\sigma\)4) that have been determined by studies on isolated fragments [12,13] or in the context of holoenzyme [14, 15, 16] (Figure 1). Domains \(\sigma\)2, \(\sigma\)3 and \(\sigma\)4 each interact with specific promoter elements and with RNAP (Figure 1). Domain \(\sigma\)2 (\(\sigma\)R1.2-2.4) is the most conserved, and forms part of an extensive interface with RNAP primarily involving an \(\alpha\)-helix comprising \(\sigma\)R2.2 and the \(\beta\)' coiled-coil [14]. During the process of DNA melting \(\sigma\)2 makes base-specific interactions with the single-stranded non-template DNA of the \(-10\) element (\(\sigma\)R2.3-2.4) thereby capturing the DNA and stabilizing RP\({}_{\circ}\) (Figure 1). The _E. coli_\(\sigma^{70}\)\(-10\) consensus sequence (T-12 ATAAT-\(\sigma\)) is particularly highly conserved at A-11 and T-\(\gamma\), since these bases are flipped out of the base stack and buried in complementary \(\sigma\)2 pockets in RP\({}_{\circ}\)[17,18] (Figure 2). In Group 1 and Group 2 \(\sigma\) factors \(\sigma\)R1.2, consisting of two \(\alpha\) helices oriented 90\({}^{\circ}\) to one another, interacts with the non-template strand \"discriminator\" element, which has an optimum sequence 5'-GGG-3' and is located immediately downstream of the \(-10\) element [18] (Figures 1 and 2). The discriminator was originally identified because its natural absence from ribosomal RNA promoters confers instability to open complexes, which facilitates regulation by the stringent factor ppGpp during nutrient stress [19, 20, 21]. Figure 1: Domain organization, promoter recognition and structural organization of the \(\sigma^{70}\) family. (**a**) The domain organization of \(\sigma\) factors from Groups 1, 3 and 4 are illustrated above \(\sigma^{70}\) (Group 1) consensus _E. coli_ promoter DNA. Structural domains are colored: \(\sigma_{1.1}\), white; \(\sigma_{2}\), green/orange; \(\sigma_{3}\), blue; \(\sigma_{4}\), red. Within each domain, conserved \(\sigma\) regions are indicated for Group 1 \(\sigma\)s. Non-template (NT) strand DNA is colored magenta and template (T) strand cyan, with key consensus promoter elements contacted by \(\sigma\) indicated in yellow: “–35”, -35 element; “ext \(-10\)”, extended \(-10\) element; “–10”, -10 element; “disc”, discriminator. Transcription initiates at \(+1\). Note that \(\sigma_{2}\) is colored green and orange to distinguish \(\sigma\) regions 2.1–2.4 and 1.2. The nonconserved region (NCR; pink) located between 1.2 and 2.1 (pink) is variable in size and structure among Group 1 \(\sigma\) factors. (**b**) Organization of _E. coli_\(\sigma^{70}\) in an RNA polymerase transcription initiation complex. The model was based on the crystal structure of an _E. coli_ transcription initiation complex (PDB: 4 YLN) [22]. \(\sigma^{70}\) domains (surface representation) and promoter DNA (spheres) are colored as in (a), as indicated in the panel. For clarity the \(\beta\), \(2\alpha\) and \(\omega\) subunits of RNA polymerase are omitted. The model indicates the location of the \(\sigma\) finger and its close proximity to nascent RNA (4 nt, yellow) and template strand DNA. Domain \(\sigma_{3}\) is a compact three-helix bundle that interacts with the major groove of duplex DNA just upstream from the \(-10\) element [24] (Figure 1). Interactions with these \"extended \(-10\)\" elements (T\({}_{\text{-15}}\)G\({}_{\text{-14}}\) in _E. coli_) can stabilize initiation complexes to such an extent that the otherwise crucial \(-35\) element is not required.