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| | **[[2mao]] – EcSF region 2 - NMR<br /> | | **[[2mao]] – EcSF region 2 - NMR<br /> |
| | **[[1tty]] – TmSF-70 region 4 – ''Thermotoga maritima''<br /> | | **[[1tty]] – TmSF-70 region 4 – ''Thermotoga maritima''<br /> |
| - | **[[1tty]] – TmSF-70 region 1.1 (mutant) - NMR<br /> | + | **[[2k6x]] – TmSF-70 region 1.1 (mutant) - NMR<br /> |
| | **[[2ahq]] – AaSF-54 C terminal – ''Aquifex aeolicus'' - NMR<br /> | | **[[2ahq]] – AaSF-54 C terminal – ''Aquifex aeolicus'' - NMR<br /> |
| | **[[2k9l]], [[2k9m]] – AaSF-54 core domain - NMR<br /> | | **[[2k9l]], [[2k9m]] – AaSF-54 core domain - NMR<br /> |
| | **[[3mzy]] – SF-H – ''Fusobacterium nucleatum''<br /> | | **[[3mzy]] – SF-H – ''Fusobacterium nucleatum''<br /> |
| | + | **[[1h3l]] – SF N terminal – ''Streptomyces coelicolor''<br /> |
| | | | |
| | *Sigma factor complex with DNA | | *Sigma factor complex with DNA |
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| | **[[2h27]] – EcSF-E region 4 + DNA<br /> | | **[[2h27]] – EcSF-E region 4 + DNA<br /> |
| | **[[2map]] – EcSF region 2 + DNA - NMR<br /> | | **[[2map]] – EcSF region 2 + DNA - NMR<br /> |
| | + | **[[1ku7]] – EcSF region 4 (mutant) + DNA <br /> |
| | **[[2o8k]], [[2o9l]] – AaSF-54 C terminal + DNA - NMR<br /> | | **[[2o8k]], [[2o9l]] – AaSF-54 C terminal + DNA - NMR<br /> |
| | | | |
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| | **[[3hug]] – MtSF + membrane protein – ''Mycobacterium tuberculosis''<br /> | | **[[3hug]] – MtSF + membrane protein – ''Mycobacterium tuberculosis''<br /> |
| | **[[4nqw]] – MtSF-K region 4 + anti-σ factor<br /> | | **[[4nqw]] – MtSF-K region 4 + anti-σ factor<br /> |
| - | **[[3wod]] – TtSF + RNAP subunits α,β,β’,ω - ''Thermus thermophilus'' <br /> | + | **[[4x8k]] – MtSF-A region 2 + RBPA<br /> |
| - | **[[4mq9]] – TtSF-70 + RNAP subunits α,β,β’,ω + antibiotic <br /> | + | **[[3wod]], [[2a6e]], [[2cw0]] – TtSF + RNAP subunits α,β,β’,ω - ''Thermus thermophilus'' <br /> |
| | + | **[[4mq9]], [[2a68]], [[2a69]], [[2a6h]], [[3dxj]], [[3eql]] – TtSF-70 + RNAP subunits α,β,β’,ω + antibiotic <br /> |
| | + | **[[2be5]] – TtSF + RNAP subunits α,β,β’,ω + inhibitor<br /> |
| | **[[1l9u]] – TaSF region 1.1-4 + RNAP subunits α,β,β’,ω<br /> | | **[[1l9u]] – TaSF region 1.1-4 + RNAP subunits α,β,β’,ω<br /> |
| - | **[[4mex]] – EcSF-70 + RNAP subunits α,β,β’,ω + antibiotic <br /> | + | **[[4yg2]] – EcSF-70 + RNAP subunits α,β,β’,ω <br /> |
| | + | **[[4mex]], [[4kmu]], [[4kn4]], [[4kn7]] – EcSF-70 + RNAP subunits α,β,β’,ω + antibiotic <br /> |
| | **[[4mey]], [[4ljz]], [[4lk1]] – EcSF-70 + RNAP subunits α,β,β’,ω <br /> | | **[[4mey]], [[4ljz]], [[4lk1]] – EcSF-70 + RNAP subunits α,β,β’,ω <br /> |
| - | **[[4lk0]], [[4llg]] – EcSF-70 + EcRNAP subunits α,β,β’,ω + RNAP inhibitor<br /> | + | **[[4lk0]], [[4llg]], [[4yfk]], [[4yfn]], [[4yfx]] – EcSF-70 + EcRNAP subunits α,β,β’,ω + RNAP inhibitor<br /> |
| | **[[4cxf]] – SF CNRH + CNRY – ''Cupriavidus metallidurans''<br /> | | **[[4cxf]] – SF CNRH + CNRY – ''Cupriavidus metallidurans''<br /> |
| | **[[4g6d]], [[4g8x]], [[4g94]] – SF-70 region 4 + Orf067 – ''Staphylococcus aureus''<br /> | | **[[4g6d]], [[4g8x]], [[4g94]] – SF-70 region 4 + Orf067 – ''Staphylococcus aureus''<br /> |
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| | **[[1rio]] - TaSF region 4 + repression protein CI + DNA<br /> | | **[[1rio]] - TaSF region 4 + repression protein CI + DNA<br /> |
| | **[[4oin]], [[4oip]], [[4oiq]], [[4oir]] – TtSF-A + RNAP subunits α,β,β’,ω + antibiotic + DNA<br /> | | **[[4oin]], [[4oip]], [[4oiq]], [[4oir]] – TtSF-A + RNAP subunits α,β,β’,ω + antibiotic + DNA<br /> |
| - | **[[4oio]] – TtSF-A + RNAP subunits α,β,β’,ω + DNA<br /> | + | **[[4oio]], [[4g7h]], [[4g7o]], [[4g7z]], [[4q4z]], [[4q5s]] – TtSF-A + RNAP subunits α,β,β’,ω + DNA<br /> |
| | + | **[[1smy]] – TtSF + RNAP subunits α,β,β’,ω + G4P<br /> |
| | **[[3n97]] – TaSF region 4 + RNAP subunits α + DNA<br /> | | **[[3n97]] – TaSF region 4 + RNAP subunits α + DNA<br /> |
| - | **[[1l9u]] – TaSF + RNAP subunits α,β,β’,ω + DNA – Cryo EM <br /> | + | **[[1l9u]], [[1l9z]] – TaSF + RNAP subunits α,β,β’,ω + DNA – Cryo EM <br /> |
| | **[[3iyd]] – EcSF-70 + EcRNAP subunits α,β,β’,ω + catabolite gene activator + DNA<br /> | | **[[3iyd]] – EcSF-70 + EcRNAP subunits α,β,β’,ω + catabolite gene activator + DNA<br /> |
| | + | **[[4jk1]], [[4jk2]], [[4jkr]] – EcSF-70 + EcRNAP subunits α,β,β’,ω + G4P<br /> |
| | + | **[[4yln]], [[4ylo]], [[4ylp]] – EcSF-70 + EcRNAP subunits α,β,β’,ω + DNA<br /> |
| | + | |
| | }} | | }} |
| | == References == | | == References == |
|
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.
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 (), 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 .
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. 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 , 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.
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1. 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.
2. Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd ed. Hoboken, NJ: Wiley, 2008.
3. 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.
