# Extracytoplasmic Function \(\sigma\) Factors as Tools for Coordinating Stress Responses
## 3 Transcription Initiation: \(\sigma^{70}\) Factor vs. ECFs  
Clearly, the regulation of \(\sigma\) factor availability and/or activity is a powerful means by which gene expression can be regulated, particularly because different RNAP holoenzymes can initiate the transcription of diverse gene clusters at the same time by swapping only one subunit. Thanks to many structural and functional studies deciphering the catalytic mechanism of RNA polymerase, many aspects related to both promoter recognition and dsDNA strand separation are known for the primary \(\sigma^{70}\) factor [23; 24; 25; 26; 27; 28; 29; 30; 31; 32; 33; 34]. More recently, a number of studies have shed light on the structures and mechanistic differences of transcriptional initiation driven by ECFs in comparison with the \(\sigma^{70}\) factor [35; 36; 37]. Taken as a paradigmatic example, _E. coli_\(\sigma^{70}\) factor (RpoD) is composed of several domains and subdomains [15; 17; 38; 39] each of them with a specific role, namely: \(\sigma_{1,1}\), \(\sigma_{2}\) (1.2, NCR, 2.1, 2.2, 2.32.4), \(\sigma_{3}\) (3.0, 3.1), \(\sigma_{3.2}\) and \(\sigma_{4}\) (4.1, 4.2) (Figure 1). Once the RNAP holoenzyme has formed, domains \(\sigma_{1,2}\), \(\sigma_{2}\), \(\sigma_{3.1}\) and \(\sigma_{4}\) of the \(\sigma^{70}\) are exposed on the surface of the holoenzyme and provide the promoter recognition and binding activity (Figure 2a). Upon promoter binding, domain \(\sigma_{2}\) triggers the separation of the dsDNA at the conserved -10 motif of the promoter to form a transcription bubble or open complex [23]. Separation of the double strand is further augmented by the region \(\sigma_{1,2}\)[40; 41], considered to be an extended part of the \(\sigma_{2}\) region [17], which melts the promoter at the discriminator element (details on the promoter melting capacity of the \(\sigma^{70}\) factor compared to ECFs are further explained at the end of this section). The \(\sigma_{\text{NCR}}\) (non-conserved region) subdomain is an adjacent region to the core \(\sigma_{2}\) domain whose interaction with the core RNAP, in a manner which is antagonistic to the core RNAP-\(\sigma_{2}\) interaction, facilitates promoter escape allowing the first stages of elongation to occur [42]. \(\sigma_{3.2}\) is a conserved linker between the \(\sigma_{3}\) and \(\sigma_{4}\) regions that inserts into the RNAP active site and occupies the RNA exit channel. Part of this region, the \(\sigma\) finger, interacts with the DNA template strand pre-organizing it into a helical conformation for accommodating it into the RNAP active site, thus enabling the binding of initiating NTPs to the template strand. For promoter escape and transcription elongation to occur, the DNA-\(\sigma_{3.2}\) interactions must be disrupted and the \(\sigma\) finger has to be displaced from the RNA exit channel, which may explain from a mechanistic perspective the close relationship between this region and abortive transcription events [23; 29; 43; 44]. As mentioned above, Group IV \(\sigma\) factors consist of only the \(\sigma_{2}\) and \(\sigma_{4}\) DNA-binding domains and a non-conserved \(\sigma_{2}\)-\(\sigma_{4}\) linker of less than 50 residues, which is highly divergent in length and sequence among ECFs. Most of the knowledge about the mechanisms of transcription initiation by ECFs comes from the well-studied _E. coli_ RpoE (\(\sigma^{\text{E}}\)). Crystal structures of RpoE \(\sigma_{4}\) complexed with the \(-35\) element [45], \(\sigma_{2}\) complexed with the \(-10\) element [46] and the structure of the transcription initiation complex formed by the RpoE-RNAP holoenzyme [35; 36; 37] have identified protein-DNA interactions critical for promoter recognition and DNA melting, and protein-protein interactions essential for the assembly of the RpoE-RNAP holoenzyme. Figure 2: Comparison between the transcription initiation mechanisms of the primary \(\sigma^{70}\) factor (RpoD) and the extracytoplasmic function \(\sigma\) factor (ECF) RpoE, from _E.