Sigma factor: Difference between revisions

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<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=''>
<StructureSection load='4lup' size='340' side='right' caption='Structure of sigma factor of E.Coli RNAP (grey) in complex with promoter DNA and ethylene glycol (PDB code [[4lup]]).' scene=''>


[[Image:2h27.jpg|left|200px]]
== Overview ==
== Overview ==


'''Sigma (σ) factor''' is the peoptide subunit needed for the initiation of RNA transcription in prokaryotic organisms <scene name='59/591940/Sigma_factor_in_enzyme/1'>as seen here</scene>.  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 <scene name='59/591940/Dna_promoter/3'>DNA promoter sequences</scene>, located upstream of transcription start sites.  
'''Sigma (σ) factor''' is the peoptide subunit needed for the initiation of RNA transcription in prokaryotic organisms <scene name='59/591940/Sigma_factor_in_enzyme/1'>as seen here</scene>.  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 <scene name='59/591940/Dna_promoter/3'>DNA promoter sequences</scene>, located upstream of transcription start sites. <br />
*'''Sigma factor 70''' or '''RpoD''' is the primary initiation factor during exponential growth.  <br />
*'''Sigma factor 45''' or '''RpoN''' is responsible for the expression of genes involved in Arg catabolism.<br />
*'''Sigma factor 38''' or '''RpoS''' acts as the master regulator of the general stress response in ''E. coli'' .<br />


== Function and Structure ==
== Function and Structure ==
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== Gene Regulation and Differentiation ==
== 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.  
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.  
</StructureSection>


==3D structures of sigma factor==
==3D structures of sigma factor==
[[Sigma factor 3D structures]]


Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
</StructureSection>
{{#tree:id=OrganizedByTopic|openlevels=0|
 
*Sigma factor
 
**[[1ku2]] – TaSF region 1.2-3.1 – ''Thermus aquaticus''<br />
**[[1ku3]] – TaSF region 4 (mutant)<br />
**[[3les]] – TaSF residues 93-271<br />
**[[1sig]] – EcSF – ''Escherichia coli''<br />
**[[2mao]] – EcSF region 2 - NMR<br />
**[[1tty]] – TmSF-70 region 4 – ''Thermotoga maritima''<br />
**[[1tty]] – TmSF-70 region 1.1 (mutant) - NMR<br />
**[[2ahq]] – AaSF-54 C terminal – ''Aquifex aeolicus'' - NMR<br />
**[[2k9l]], [[2k9m]] – AaSF-54 core domain - NMR<br />
**[[3mzy]] – SF-H – ''Fusobacterium nucleatum''<br />
 
*Sigma factor complex with DNA
 
**[[3ugo]], [[3ugp]] - TaSF region 2 + DNA<br />
**[[4ki2]] - TaSF region 2-3 + DNA<br />
**[[2h27]] – EcSF-E region 4 + DNA<br />
**[[2map]] – EcSF region 2 + DNA - NMR<br />
**[[2o8k]], [[2o9l]] – AaSF-54 C terminal + DNA - NMR<br />
 
*Sigma factor complex with protein
 
**[[3lev]] – TaSF residues 93-271 + antibody<br />
**[[1or7]] – EcSF-E + σ-E factor negative regulatory protein <br />
**[[4lup]] – EcSF residues 3-92 + EcSF region 2 <br />
**[[1tlh]] – EcSF-70 region 4 + anti-σ factor<br />
**[[2p7v]] – EcSF-70 region 4 + regulator of σ D<br />
**[[1rp3]], [[1sc5]] – AaSF-28 + anti-σ factor FLGM <br />
**[[3hug]] – MtSF + membrane protein – ''Mycobacterium tuberculosis''<br />
**[[4nqw]] – MtSF-K region 4 + anti-σ factor<br />
**[[3wod]] – TtSF + RNAP subunits α,β,β’,ω - ''Thermus thermophilus'' <br />
**[[4mq9]] – TtSF-70 + RNAP subunits α,β,β’,ω + antibiotic <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 />
**[[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 />
**[[4cxf]] – SF CNRH + CNRY – ''Cupriavidus metallidurans''<br />
**[[4g6d]], [[4g8x]], [[4g94]] – SF-70 region 4 + Orf067 – ''Staphylococcus aureus''<br />
 
*Sigma factor complex with protein and DNA


**[[1rio]] - TaSF region 4 + repression protein CI + 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 />
**[[3n97]] – TaSF region 4 + RNAP subunits α + DNA<br />
**[[1l9u]] – 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 />
}}
== References ==
== References ==


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