# Extracytoplasmic Function \(\sigma\) Factors as Tools for Coordinating Stress Responses
## 2 Bacterial \(\sigma\) Factor Families  
When considered from a structural point of view, \(\sigma\) factors can be divided in two main, structurally unrelated families: one large group includes the primary \(\sigma^{70}\) family, and the other much smaller group includes the RpoN family (classically known as \(\sigma^{54}\) or \(\sigma^{\text{N}}\)), [13; 14]. The RpoN family is generally represented by one member per bacterial genome. Although the difference between these two families is not the main focus of this review, it is nevertheless important to stress that RpoN acts in concert with ATP-dependent activators to help unwind the double-stranded DNA (dsDNA) near the transcription start site (TSS) to initiate transcription. In contrast, RNAP holoenzymes formed with \(\sigma^{70}\) family members melt the DNA near the TSS in an ATP-independent manner and without the aid of additional regulatory proteins [15]. The \(\sigma_{2}\) domain is able to melt the DNA at the -10 box once the RNAP holoenzyme is correctly positioned thanks to the DNA-binding activity of \(\sigma_{4}\) and \(\sigma_{3}\) domains to other promoter regions, such as the -35 box and the extended -10 region, respectively [16]. These structural domains, plus another additional domain with non-essential activity for promoter binding (\(\sigma_{1,1}\)), form the basis of the typical structure feature of the primary \(\sigma^{70}\) factor, ascribed to Group I (Figure 1). \(\sigma\) factors belonging to Groups II-IV are considered alternative, because they are usually not essential for cell viability and may diverge from Group I in the presence of certain domains. Group II \(\sigma\) factors, with one well-characterized example in _Escherichia coli_ RpoS, conserve the same domain architecture as the primary \(\sigma^{70}\) factor (RpoD in _E. coli_) except for the absence of the region \(\sigma_{1,1}\)[17], and their absence does not result in lethality. Thus, they are generally defined as non-essential \(\sigma^{70}\) homologs. Members of Group III, such as _E. coli_ RpoH and FliA, essentially conserve domains \(\sigma_{2}\), \(\sigma_{3}\) and \(\sigma_{4}\)[17]. Although \(\sigma_{3}\) and \(\sigma_{4}\) bind different promoter regions, they are considered redundant, since the RNAP holoenzyme can bind and orientate efficiently in the absence of one of these domains or one of their DNA-binding determinants [16]. ECFs comprise Group IV with their structure being determined by the presence of only domains \(\sigma_{2}\) and \(\sigma_{4}\) separated by a linker shorter than 50 residues. Actually, \"Group IV\" would be a more appropriate term to describe these \(\sigma\) factors, since it is meanwhile clear that some ECFs respond to intracellular stimuli [13]. Classification of \(\sigma^{70}\) family members has relied on the presence of various well-conserved protein domains and subdomains (Figure 1). However, in some cases, the boundaries of this classification are diffuse, as some proteins may act as \(\sigma\) factors despite showing low similarity or a different organization, or vice versa, some proteins may have a structure resembling a \(\sigma\) factor whilst not functioning as such. For instance, a group of proteins encoded by _Clostridium_ species that control the production of extracellular toxins, such as TcdR or BotR, function as \(\sigma\) factors at the biochemical level, and even show somewhat recognizable \(\sigma_{2}\) and \(\sigma_{4}\) domains [18; 19]. However, the marked sequence divergence from Group IV representatives prevents a clear-cut classification into that group. This led to the proposition of these proteins as members of a novel category (Group V), branching from Group IV. Another example of these hard-to-define \(\sigma\) elements is the SigO-RsoA system, formerly YvrI-YvrHa [20; 21].