Sigma factor

<StructureSection load='4lup' size='340' side='right' caption='Structure of sigma factor of E.Coli RNAP in complex with Promoter DNA (PDB code 4lup).' scene=>

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.

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 (HTH), 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 TATAAT.

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 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. 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.

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