Chapter 1 General Introduction Figure 2. Activation of the E. Coli Ecf Sigma Factor Σ Activation of Stress Responsive (rpoe-like) Σ Activation of Iron Starvation (feci-like) Σ

70 family of sigma factors. Regulation of gene expression is an essential mechanism that allows bacteria to rapidly adapt to alterations in their environment. In this way, they preserve energy and profit by expressing particular genes only when required. Gene expression in bacteria is regulated primarily at the level of transcription initiation by modulating promoter recognition of the RNA polymerase (RNAP) holoenzyme. The bacterial RNAP holoenzyme is composed of a five-subunit core enzyme (RNAPc; subunit composition α2ββ'ω) and a dissociable sigma (σ) subunit (Murakami and Darst, 2003). Whereas the core of the RNA polymerase has enzyme activity, the sigma factor contains most promoter recognition determinants and confers promoter specificity to the RNA polymerase. The sigma factor is also required for transcription initiation, which is a stepwise process. First, the RNAP holoenzyme forms a closed complex around the promoter in which the DNA is double-stranded. After isomerisation (melting) of the DNA around the transcription start point, an open complex is formed and transcription commences (Browning and Busby, 2004). Following transcription initiation, the σ factor dissociates from the RNAP and is available to interact with a next core enzyme complex, while the remaining RNAPc drives RNA transcription until a transcription termination site is encountered (Mooney et al., 2005). All bacteria contain a primary sigma factor that directs transcription of general housekeeping genes. Specific activator or repressor proteins can affect binding of primary sigma factor-containing RNAP complexes and as such regulate promoter activity. However, in addition most bacteria also encode several alternative σ factors, which can redirect the RNAP to initiate transcription from specific sets of alternative promoters (Helmann and Chamberlin, 1988). By alternating the use of standard and alternative sigma factors bacteria are able to adequately regulate general cell functions as well as responses to specific signals. Therefore, the versatility and adaptability of bacteria is partially reflected by the number of alternative sigma factors they produce (Paget and Helmann, 2003). Bacterial sigma factors have been classified into two main and unrelated families, namely the σ 70 and the σ 54 families. σ 54-type sigma factors are structurally different from σ 70 family members and utilize a different mechanism of open complex formation (Merrick, Figure 1. Structure of the σ 70 family of sigma factors. The four conserved regions with the subregions as well as the non-conserved region (NCR) of Group 1 sigma factors are drawn. A typical promoter with-10, extended-10 and-35 boxes …