## 3 _E. coli_\(\sigma\)[70] Promoter Recognition
This strong bend observed in solution may be due to \(\mathfrak{s}_{4}\) interacting with the \(\alpha\)CTDs [12, 81]. At some promoters, \(\mathfrak{s}_{4}\) interacts with activators such as \(\lambda\)CI [82] and CAP [11, 83, 84, 85], influencing multiple steps of transcription initiation. This region can also interact with the core RNAP to mediate recruitment of elongation factors [86]. There is no consensus sequence for the majority of the spacer between the \(-35\) and \(-10\) elements, but there is a consensus length, which is dictated largely by the spacing between \(\mathfrak{s}_{4.2}\) and \(\mathfrak{s}_{2.3}\)[13]. The most common spacer length for \(\mathfrak{s}^{70}\) promoters is \(17\) bp [79, 87, 88], and promoters with \(17\) bp spacers produce greater amounts of transcript in multi-round assays than otherwise identical promoters [89, 90, 91]. The length and extent of bending (as predicted by molecular modeling) of the spacer region modulate the effect of \(\mathfrak{s}_{1.1}\) on transcription initiation kinetics and the structure of the open complex [92]; the underlying mechanism is unknown, but the authors speculate that this may be due to \(\mathfrak{s}_{1.1}\) acting as a \"gatekeeper\", discriminating between promoter and non-promoter DNA based on the trajectory of the spacer from the \(-35\) element to the \(-10\). Recent structures of _E. coli_\(\mathfrak{s}^{70}\) initiation complexes formed with \(4\)-\(5\) nt nascent RNAs reveal that rotation of \(\mathfrak{s}_{4}\) is required to accommodate different promoter spacer lengths [77]. A region within the spacer defined as the \"Z-element\" (bases \(-24\) to \(-18\)) was also identified in a recent study as interacting with the \(\beta\)' zipper (residues 40-45), increasing the amount of abortive transcription from a synthetic promoter [93]. It is not known, however, whether this interaction is sequence-specific or simply specific to a certain spacer conformation or trajectory. At some promoters, an \"extended \(-10\)\" sequence (TGn; Figure 1, red) increases activity through specific contacts with \(\mathfrak{s}_{3.0}\)[44, 94] (Figures 1 and 2, red), perhaps by increasing the lifetime of the open complex [95]. The TGn motif was found in \(20\%\) of the \(554\) promoters identified in one study [87], with \(44\%\) of these promoters having a G at \(-14\). The TGn motif may be particularly important at promoters with weaker \(-35\) elements [43] or longer spacers [87]. In _E. coli_ initiation complex structure, the extended \(-10\) element is recognized by the insertion of two perpendicular helices of \(\mathfrak{s}_{2}\) and \(\mathfrak{s}_{3}\) into the major groove [77]. The \(-10\) element (Figure 1, yellow), with an all-AT bp consensus sequence (5'-TATAAT-3') constitutes the upstream half of the region opened by RNAP, with opening likely initiated near its upstream end. The transcription bubble forms downstream of base \(-12\) (for \(\lambda\)P\({}_{\textrm{R}}\) and other promoters with six bp discriminators; see Figure 1). This position remains base paired [77, 96], with the _E. coli_\(\mathfrak{s}^{70}\) Q437 likely making a key sequence-specific contact [97] with base \(-12\)A of the template strand [10]. After opening, the \(-10\) region of the nontemplate strand interacts with conserved residues of \(\mathfrak{s}\), with the nearly invariant bases \(-11\)A and \(-7\)T in pockets of \(\mathfrak{s}^{70}\)[10, 17, 98, 99]. Residues of both template and nontemplate strands interact with \(\mathfrak{s}_{2.4}\)[10, 17]. Modeling and biochemical data suggest that these contacts require prior strand separation [10]. It remains unresolved whether recognition of this region requires the DNA to be single-stranded. The base \(-11\)A is thought to nucleate DNA opening; alanine substitutions of aromatic residues in the \(-11\)A binding pocket on \(\sigma_{2.3}\) impair open complex formation, but not binding to duplex DNA [100].