Sigma factor

Overview

Sigma (σ) factor is the peoptide subunit needed for the initiation of RNA transcription in prokaryotic organisms . 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 , located upstream of transcription start sites.

Specific 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." 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. 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, is referred to as the σ cycle.

Domains

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). 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 (), helps specifically recognize DNA promoters at both the -35 and -10 positions. 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, such as .

Restriction

Normally, σ-factor domains cannot bind to promoters. 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. Additionally, in housekeeping σs, a domain called the σ(1.1) stabilizes the compact conformation mentioned above, thereby preventing any promoter recognition.

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.

Transcription Bubble

The , 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. As such, σ factors require invariant basic and aromatic residues (Phe, Tyr, Trp) critical for this formation. The process of bubble formation begins at the -11 formation (usually A) and propogates to +1 site, through "base flipping" which interrupts the stacking interactions stabilizing the double helix conformation. As a result, -35 and -10 motif sequence recognition and strand separation are both coupled by the σ factor.

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 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. This process of σ-factor cascades demonstrates the versatile and essential biologic functions of the RNAP subunit, σ.

3D structures of sigma factor

Updated on 14-October-2014

Sigma factor

1ku2 – TaSF region 1.2-3.1 – Thermus aquaticus
1ku3 – TaSF region 4 (mutant)
3les – TaSF residues 93-271
1sig – EcSF – Escherichia coli
2mao – EcSF region 2 - NMR
1tty – TmSF-70 region 4 – Thermotoga maritima
1tty – TmSF-70 region 1.1 (mutant) - NMR
2ahq – AaSF-54 C terminal – Aquifex aeolicus - NMR
2k9l, 2k9m – AaSF-54 core domain - NMR
3mzy – SF-H – Fusobacterium nucleatum

Sigma factor complex with DNA

3ugo, 3ugp - TaSF region 2 + DNA
4ki2 - TaSF region 2-3 + DNA
2h27 – EcSF-E region 4 + DNA
2map – EcSF region 2 + DNA - NMR
2o8k, 2o9l – AaSF-54 C terminal + DNA - NMR

Sigma factor complex with protein

3lev – TaSF residues 93-271 + antibody
1or7 – EcSF-E + σ-E factor negative regulatory protein
4lup – EcSF residues 3-92 + EcSF region 2
1tlh – EcSF-70 region 4 + anti-σ factor
2p7v – EcSF-70 region 4 + regulator of σ D
1rp3, 1sc5 – AaSF-28 + anti-σ factor FLGM
3hug – MtSF + membrane protein – Mycobacterium tuberculosis
4nqw – MtSF-K region 4 + anti-σ factor
3wod – TtSF + RNAP subunits α,β,β’,ω - Thermus thermophilus
4mq9 – TtSF-70 + RNAP subunits α,β,β’,ω + antibiotic
1l9u – TaSF region 1.1-4 + RNAP subunits α,β,β’,ω
4mex – EcSF-70 + RNAP subunits α,β,β’,ω + antibiotic
4mey, 4ljz, 4lk1 – EcSF-70 + RNAP subunits α,β,β’,ω
4lk0, 4llg – EcSF-70 + EcRNAP subunits α,β,β’,ω + RNAP inhibitor
4cxf – SF CNRH + CNRY – Cupriavidus metallidurans
4g6d, 4g8x, 4g94 – SF-70 region 4 + Orf067 – Staphylococcus aureus

Sigma factor complex with protein and DNA

1rio - TaSF region 4 + repression protein CI + DNA
4oin, 4oip, 4oiq, 4oir – TtSF-A + RNAP subunits α,β,β’,ω + antibiotic + DNA
4oio – TtSF-A + RNAP subunits α,β,β’,ω + DNA
3n97 – TaSF region 4 + RNAP subunits α + DNA
1l9u – TaSF + RNAP subunits α,β,β’,ω + DNA – Cryo EM
3iyd – EcSF-70 + EcRNAP subunits α,β,β’,ω + catabolite gene activator + DNA

References

Felklistov, Andrey, Brian D. Sharon, Seth A. Darst, and Carol A. Gross. "Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective." The Annual Review of Microbiology 68 (2014): 357-76.

Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd ed. Hoboken, NJ: Wiley, 2008.

Mooney, R. A., S. A. Darst, and R. Landick. "Sigma and RNA Polymerase: An On-again, Off-again Relationship?" Molecular Cell 20.3 (2005): 335-45.