Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution

Abstract

Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (Group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (Groups 2-4) that control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. Sigma factors are then released through a wide variety of mechanisms, often involving branched signal transduction pathways that allow the integration of distinct signals. Three major strategies for sigma release are discussed: regulated proteolysis, partner-switching, and direct sensing by the anti-sigma factor.

Keywords: RIP; RNA polymerase; anti-sigma; extracytoplasmic; partner-switching; sigma; signal transduction; stress; transcription.

Figure 1

Domain organization, promoter recognition and structural organization of the σ⁷⁰ family. (a) The domain organization of σ factors from Groups 1, 3 and 4 are illustrated above σ⁷⁰ (Group 1) consensus E. coli promoter DNA. Structural domains are colored: σ_1.1, white; σ₂, green/orange; σ₃, blue; σ₄, red. Within each domain, conserved σ regions are indicated for Group 1 σs. Non-template (NT) strand DNA is colored magenta and template (T) strand cyan, with key consensus promoter elements contacted by σ indicated in yellow: “−35”, −35 element; “ext −10”, extended −10 element; “−10”, −10 element; “disc”, discriminator. Transcription initiates at +1. Note that σ₂ is colored green and orange to distinguish σ regions 2.1–2.4 and 1.2. The nonconserved region (NCR; pink) located between 1.2 and 2.1 (pink) is variable in size and structure among Group 1 σ factors. (b) Organization of E. coli σ⁷⁰ in an RNA polymerase transcription initiation complex. The model was based on the crystal structure of an E. coli transcription initiation complex (PDB: 4YLN) [22]. σ⁷⁰ domains (surface representation) and promoter DNA (spheres) are colored as in (a), as indicated in the panel. For clarity the β, 2α and ω subunits of RNA polymerase are omitted. The model indicates the location of the σ finger and its close proximity to nascent RNA (4 nt, yellow) and template strand DNA.

Figure 2

Interactions of E. coli σ⁷⁰ and σ^E with “flipped out” bases in non-template strand of −10 regions. The σ⁷⁰-DNA model is a partial representation of a crystal structure of an E. coli σ⁷⁰ transcription initiation complex (PDB: 4YLN) [22] showing the σ⁷⁰₂ domain interactions with the non-template strand (C_-13T_-12A_-11T_-10A_-9A_-8T_-7G_-6T_-5G_-4) Flipped out bases in the −10 element (−11A and −7T) and the discriminator element (−6G) are indicated. Note that DNA upstream of −11A is double stranded, with the template strand not shown for clarity. The σ^E-DNA model is based on a crystal structure of the E. coli σ^E₂ domain bound to a non-template strand oligonucleotide (PDB: 4LUP) [23] based on the σ^E consensus −10 sequence (T_-13G_-12T_-11C_-10A_-9A_-8A_-7). The modular loop that interacts with the flipped out −10C is indicated. σ₂ domains are illustrated in surface representation with conserved regions colored as indicated and the σ⁷⁰ NCR not shown.

Figure 3

The inhibition of σ activity by anti-σ factors. A comparison between complexes of σ^E-RseA (PDB: 1OR7-2) and a σ^CnrH/CnrY/ (PDB: 4CXF). The σ₂ and σ₄ domains are colored green and red, respectively. The anti-sigma binding domains of RseA and CnrY are colored blue.

Figure 4

Mechanisms for σ factor release from anti-σ factors. (a) Activation of σ^E in E. coli. The membrane-spanning anti-σ RseA binds σ^E through its cytoplasmic ASD. The C-termini of OMPs that accumulate in the periplasm activate DegS protease through binding to its PDZ domain, resulting in site-1 cleavage of RseA. DegS–dependent cleavage of RseA is inhibited by RseB, and this can be relieved by the accumulation of lipopolysaccharide (LPS) in the periplasm that binds directly to RseB. Site-1 cleavage is sensed by RseP, which subsequently catalyzes site-2 cleavage of RseA on the cytoplasmic side of the membrane, releasing a soluble σ^E/RseA complex. σ^E is released when the RseA ASD is finally degraded by ATP-dependent proteases such as ClpXP. (b) Activation of σ^R in S. coelicolor. RsrA binds to and inactivates σ^R via its ZASD domain. The RsrA zinc ion is coordinated by three cysteine (C) residues and one histidine (H). In response to oxidative stress, RsrA forms at least one disulphide bond, which concomitantly displaces the zinc and causes a structural change that prevents σ^R binding. The system can be reset by the reduction of RsrA by cellular thiol-disulphide oxidoreductases such as thioredoxin that are activated by σ^R. (c) Activation of σ^B in B. subtilis. RsbW is an anti-σ factor/kinase that binds to σ^B, and additionally inactivates its alternative binding partner RsbV by phosphorylating it to RsbV-P. Activation of σ^B occurs by partner-switching when RsbV-P is dephosphorylated by alternative phosphatases (RsbTU or RsbQP) in response to environmental or energy stresses, which allows RsbV to bind and sequester RsbW.