Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors

Abstract

The ECF sigma family was identified 23 years ago as a distinct group of σ⁷⁰-like factors. ECF sigma factors have since emerged as a major form of bacterial signal transduction that can be grouped into over 50 phylogenetically distinct subfamilies. Advances in our understanding of these sigma factors and the signaling pathways governing their activity have elucidated conserved features as well as aspects that have evolved over time. All ECF sigma factors are predicted to share a common streamlined domain structure and mode of promoter interaction. The activity of most ECF sigma factors is controlled by an anti-sigma factor. The nature of the anti-sigma factor and the activating signaling pathways appear to be conserved within ECF families, while considerable diversity exists between different families.

Figure 1

Promoter recognition by ECF sigma factors. (a) Domain 2 from σ^E_Ec bound to the nontemplate strand of the −10 promoter element is shown. Protein helices are in red and loops are in gray, while promoter DNA is in blue. The loop that determines binding specificity is indicated. It forms a pocket for the cytosine base, shown in ball and stick format, that is flipped out from the ssDNA helix. (b) Domain 4 from σ^E_Ec bound to the −35 promoter element is shown. Protein helices are in green and loops in gray. (c) Schematic of conserved regions of ECF and primary sigma factors are diagrammed. Interactions between individual sigma factor domains and the promoter are indicated by dashed lines. NCR is the nonconserved region of primary sigma factors. Disc. is the discriminator motif and ext. −10 is the extended −10 motif. Structural representations were generated from PDB 4LUP [17] and 2H27 [16] using Chimera [44].

Figure 2

Structural conservation of the ASD from ChrR, RseA, RskA, and RsiW. Structural alignments were performed using Swiss-PDBViewer 4.0 and displayed using Chimera [71]. The three-helix bundle is superimposable for all the anti-sigma factors, while the position of the fourth helix is variable. ChrR is shown in cyan, RseA in green, RskA in orange, and RsiW in red.

Figure 3

Two modes of sigma factor/anti-sigma factor interactions. Structures of σ^E_Ec bound to RseA (top left), σ^K_Mtb bound to RskA (top center), σ^E_Rs bound to ChrR (top right), σ^W_Bs bound to RsiW (bottom left), and CnrH bound to CnrY (bottom center) are shown. Domains 2 and 4 of the sigma are in red and green, respectively. The anti-sigma factors are shown in turquoise. For ChrR, ChrR-ASD is the N-terminal anti-sigma domain and ChrR-CLD is the C-terminal cupin-like domain. A cartoon representation of the two binding modes is shown (bottom right). Structural representations were generated from PDB 1OR7 [27], 2Q1Z [26], 4NQW [30^•], 5WUQ [29] and 4CXF [35^••] using Chimera [71].

Figure 4

Envelope sensing by regulated proteolysis and redox sensing by conformational changes. (a) Roles of the key players in the pathways regulating σ^E_Ec and AlgU are depicted as the system transitions from the inactive to the active state. Proteolysis of RseA and MucA is triggered by binding of OMP peptides to DegS and AlgW in conjunction with release RseB and MucB from the anti-sigma factor upon LPS binding. For P. aeruginosa, CupB5 can activate AlgW bypassing the need for LPS binding to MucB. (b) Activation of σ^V by degradation of RsiV following lysozyme binding is depicted. In the inactive state, the first protease to act, signal peptidase, cannot access RsiV. Binding of lysozyme to RsiV exposes the cleavage site in RsiV to signal peptidase initiating the proteolytic cascade. (c) A related proteolytic pathway regulates degradation of the RsmA, RskA, and RslA anti-sigma factors from M. tuberculosis. The initiating protease and inducing signals have yet to be identified. Rip1 is responsible for the second cleavage in the proteolytic cascade for all three anti-sigma factors. The adapter protein, Ppr1, bridges Rip1 and RsmA and prevents cleavage. Similar adapter proteins have been postulated for RskA and RslA. (d) Redoxing sensing by RsrA is depicted. In the inactive state, σ^R is sequestered by the reduced Zn bound form of RsrA. Exposure to reactive electrophile species results in loss of Zn, formation of an intramolecular disulfide bond, structural rearrangement of RsrA, and release of σ^R. (e) Activation of σ^E by singlet oxygen (¹O₂). In the inactive state, σ^E is bound to ChrR. Singlet oxygen sensing involves ligands of the Zn atom in the ChrR-CLD, although loss of Zn is not absolutely required, and leads to degradation of ChrR by an unknown mechanism.