# Extracytoplasmic Function \(\sigma\) Factors as Tools for Coordinating Stress Responses
## 3 Transcription Initiation: \(\sigma^{70}\) Factor vs. ECFs
coli._ (**a**) Involvement of the different \(\sigma\) factor domains (using the same color code as in Figure 1) in the transcription initiation, emphasizing the differences between the vegetative \(\sigma^{70}\) factor and RpoE regarding their promoter melting capability. The different isomerization stages from closed complex to open complex are indicated. (**b**) Schematic of the contacts between -10 box nucleotides and \(\sigma_{2}\) domain residues for RpoD and RpoE. Residues directly interacting with -10 box nucleotides are underlined. Nucleotides that are flipped-out during transcription initiation and the respective residues that contact them are indicated in red. Apart from the differences in the interaction with the -10 box between ECFs and primary [70] factors, divergent mechanisms for the recognition of the conserved -35 sequence motif have also been described [45; 47]. In Group I factors, abundant nucleotide-speci c interactions are stablished between the \({}_{4}\) domain and the -35 box, for example, using the Thermus aquaticus [70] factor as a model for structural studies [45]. When determining the interaction between the \({}_{4}\) domain of the ECFs RpoE (E. coli) and SigW (B. subtilis, with target -35 boxes GGAACTT and ATTGAAACCTTT, respectively, numerous additional interactions also occurred, except with the central short A-tract [45; 47]. Interactions with the A-tract happened to be fewer and weaker, which contrasts with the widespread conservation of the central A-tract in the target -35 box of most ECFs. The explanation for this, which is suggested to apply for other ECFs, is that the presence of this A-tract provides the appropriate DNA geometry within the -35 box for its interaction with the \({}_{4}\) domain. The recent structural studies of transcription initiation complexes using the Mycobacteriumrium tuberculosis \({}^{\rm H}\), \({}^{\rm L}\) and chimeric \({}^{\rm H}\)/\({}^{\rm E}\) factors revealed that the \({}_{2^{*}}\) -\({}_{4}\) linker, similarly to the aforementioned \({}_{\rm\  
according to [46]). Swapping this \"speci city loop L3\" of E. coli RpoE for the respective loops of Bacillus subtilis W, X or Sphingomonas microfSciG redirected the speci city of the RNAP holoenzyme to the target sequence of those factors, which only differ in the -10 nucleotides. Altogether, this explains the reduced melting capacity and high promoter stringency of ECFs, which prevents non-speci c transcription initiation, in contrast to primary 70 factors, characterized by a high promoter-melting capacity required to drive the bulk of bacterial transcription from promoters where A -11 and T.-7, and additionally G -6, are conserved [46, 49]. These speci c ECF-promoter interactions at the -35 and -10 boxes have been recently explored to implement a tool for promoter prediction based on the amino acid composition of key DNA contact points within the 2 and 4 domains [50]. Its application has allowed the prediction of target regulons of nearly 70% of the known ECFs and established that around 55% of them are autoregulated.