Sigma factor

Overview

Sigma (σ) factor is the peoptide subunit needed for the initiation of RNA transcription in prokaryotic organisms as seen here. As opposed to eukaryotes, who utilize a variety of proteins to initiate gene transcription, prokaryotic transcription is initiated almost completely by a σ-factor. The large and biologically essential protein, RNA polymerase (RNAP), contains one σ-subunit, which binds DNA promoter sequences, located upstream of transcription start sites.

• Sigma factor 70 or RpoD is the primary initiation factor during exponential growth.
  
• Sigma factor 45 or RpoN is responsible for the expression of genes involved in Arg catabolism.
  
• Sigma factor 38 or RpoS acts as the master regulator of the general stress response in E. coli .
  

Function and Structure

The σ-factor performs two chief functions: to direct the catalytic core of RNAP to the promotoer upstream of the +1 start site of transcription, and finally to assist in the initiation of strand seperation of double-helical DNA, forming the transcription "bubble."[1] Each gene promoter utilizes a specific promoter region about 40 bp upstream of the transcription start site, and therefore different σ-factors play a role in the regulation of different genes [2]. This process, which includes association of the σ-factor with RNAP to recognize and open DNA at the promoter site, followed by dissociation of the σ to allow elongation, which can then activate additional RNAP enzymes, is referred to as the σ-cycle [3].

Domain Strucure & DNA interactions

There are many types of σ-subunits, and each recognizes a unique promoter sequence. Furthmore, each unique σ is composed of a variable number of structured domains. The simplest σ-factors have two domains, few have three, and most, called housekeeping σ-factors, have 4 domains, given the names σ(4), σ(3), σ(2), and σ(1.1) [1,3]. All domains are linked by very flexible peptide linkers which can extend very long distances. Each of these domains utilizes DNA-binding determinants, or domains that recognize specific sequences and conformations in DNA. Most commonly, these recognized sequences occur at the -35 and -10 locations upstream of the +1 site. One such DNA-binding motif, the helix-turn-helix motif (HTH), helps specifically recognize DNA promoters at both the -35 and -10 positions [1]. This HTH motif, used by most σ-factors, maintains its specificity and accuracy by binding in the major groove of DNA, where it can interact with the base pairs in the DNA double-helix. In many prokaryotes, these portions of DNA maintain consensus adenosine and thymine sequences [1,2], such as TATAAT.

Transcription Bubble

The transcription bubble, also referred to as the open complex is formed through the common housekeeping σ factors which unwind about 13 bp of duplex DNA in an ATP independent process. Research has shown that σ factors require invariant basic and aromatic residues (Phe, Tyr, Trp) critical for this formation [1]. The process of bubble formation begins at the -11 formation (usually A) and propogates to +1 site, through a phenomenon called Base Flipping, which interrupts the stacking interactions stabilizing the double helix conformation [1]. As this process occurs and the DNA transitions into the open promoter complex, certain RNAP-σ contacts are lost, initiating the dissociation of σ. In summary, the processes of -35 and -10 motif sequence recognition and helix strand separation are coupled by the σ factor.

Restriction

Initiation of prokaryotic transcription requires cooperation between the σ peptide and RNAP. Without these fundamental interactions, no transcription is possible.

Comformational and Autoinhibitory

Normally, σ-factor domains cannot bind to promoters on their own. These domains usually are placed in very compacted positions relative to each other, a conformation that buries DNA-binding determinants. This type of restriction is called conformational restriction[1]. Additionally, in housekeeping σs, a domain called the σ(1.1) stabilizes the compact conformation mentioned above, thereby preventing any promoter recognition. This method of restricting the binding abilities of isolated σ's is called autoinhibitory inhibition[1].

anti-σ's

An additional method of restriction is through the action of anti-σ's, which act by making stable interactions with σ-domains, such as σ (4), which allows them to make energy-favorable interactions with RNAP residues. This causes a cascading "peeling off" effect of other σ-domains from the RNAP, preventing any interaction with duplex DNA and inhibiting transcription in an analogous process to competitive inhibition [3].

Gene Regulation and Differentiation

Since σ-factors are exclusively linked to gene expression in prokaryotic organisms, the variety of σ-factors in a cell dictate how and what genes are transcribed. Specialized function in cells, therefore, is highly moderated by its arsenal of σ-subunits. In fact, cellular development and differentiation are directly impacted and carried out by "cascades" of σ-factors. In the early stages of development, early genes[2] are transcribed by basic bacterial σ-factors. These genes are therefore transcribed to give new σ-factors, which in turn activate additional genes, and so on [2]. This process of σ-factor cascades demonstrates the versatile and essential biologic functions of the RNAP subunit, σ.

3D structures of sigma factor

Sigma factor 3D structures