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Sigma factor

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== Overview ==
== Overview ==
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'''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.
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'''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 />
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*'''Sigma factor 70''' or '''RpoD''' is the primary initiation factor during exponential growth. <br />
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*'''Sigma factor 45''' or '''RpoN''' is responsible for the expression of genes involved in Arg catabolism.<br />
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*'''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.
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</StructureSection>
 
==3D structures of sigma factor==
==3D structures of sigma factor==
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[[Sigma factor 3D structures]]
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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</StructureSection>
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*Sigma factor
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**[[1ku2]] – TaSF region 1.2-3.1 – ''Thermus aquaticus''<br />
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**[[1ku3]] – TaSF region 4 (mutant)<br />
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**[[3les]] – TaSF residues 93-271<br />
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**[[1sig]] – EcSF – ''Escherichia coli''<br />
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**[[2mao]] – EcSF region 2 - NMR<br />
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**[[1tty]] – TmSF-70 region 4 – ''Thermotoga maritima''<br />
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**[[2k6x]] – TmSF-70 region 1.1 (mutant) - NMR<br />
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**[[2ahq]] – AaSF-54 C terminal – ''Aquifex aeolicus'' - NMR<br />
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**[[2k9l]], [[2k9m]] – AaSF-54 core domain - NMR<br />
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**[[3mzy]] – SF-H – ''Fusobacterium nucleatum''<br />
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**[[1h3l]] – ScSF N terminal – ''Streptomyces coelicolor''<br />
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**[[5fgm]] – ScSF-R region 4<br />
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**[[5mww]] – BsSF-A region 1.1 - ''Bacillus subtilis'' - NMR <br />
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**[[5xe7]] – MtSF-J – ''Mycobacterium tuberculosis''<br />
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*Sigma factor complex with DNA
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**[[3ugo]], [[3ugp]] - TaSF region 2 + DNA<br />
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**[[4ki2]] - TaSF region 2-3 + DNA<br />
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**[[2h27]] – EcSF-E region 4 + DNA<br />
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**[[2map]] – EcSF region 2 + DNA - NMR<br />
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**[[1ku7]] – EcSF region 4 (mutant) + DNA <br />
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**[[2o8k]], [[2o9l]] – AaSF-54 C terminal + DNA - NMR<br />
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**[[5ui5]] – AaSF RpoN residues 61-398 + DNA <br />
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*Sigma factor complex with protein
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**[[3lev]] – TaSF residues 93-271 + antibody<br />
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**[[1or7]] – EcSF-E + σ-E factor negative regulatory protein <br />
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**[[4lup]] – EcSF residues 3-92 + EcSF region 2 <br />
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**[[1tlh]] – EcSF ProD region 4 + anti-σ factor<br />
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**[[2p7v]] – EcSF ProD region 4 + regulator of σ D<br />
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**[[1rp3]], [[1sc5]] – AaSF-28 + anti-σ factor FLGM <br />
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**[[5wuq]] – BsSF SIGW + anti-σ factor RSIW <br />
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**[[3hug]] – MtSF-L + membrane protein <br />
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**[[4nqw]] – MtSF-K region 4 + anti-σ factor<br />
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**[[4x8k]] – MtSF-A region 2 + RBPA<br />
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**[[6fbv]] – MtSF-A + RNAP subunits α,β,β’,ω - SP Cryo EM<br />
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**[[6c05]], [[6c06]] – MtSF-A + RNAP subunits α,β,β’,ω + RbpA - Cryo EM<br />
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**[[3wod]], [[2a6e]], [[2cw0]], [[5tmf]] – TtSF + RNAP subunits α,β,β’,ω - ''Thermus thermophilus'' <br />
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**[[4mq9]], [[2a68]], [[2a69]], [[2a6h]], [[3dxj]], [[3eql]] – TtSF ProD + RNAP subunits α,β,β’,ω + antibiotic <br />
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**[[2be5]] – TtSF + RNAP subunits α,β,β’,ω + inhibitor<br />
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**[[5tmc]] – TtSF-A + RNAP subunits α,β,β’,ω + protein + G4P<br />
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**[[5xj0]] – TtSF-A + RNAP subunits α,β,β’,ω + GP39 + GP76<br />
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**[[5x22]] – TtSF-A + RNAP subunits α,β,β’,ω + GpA + CMPcPP<br />
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**[[1l9u]] – TaSF region 1.1-4 + RNAP subunits α,β,β’,ω<br />
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**[[4yg2]], [[5uag]], [[5uaj]], [[5uaq]] – EcSF ProD + RNAP subunits α,β,β’,ω <br />
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**[[5ui8]] – EcSF-45 + RNAP subunits α,β,β’,ω <br />
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**[[4mex]], [[4kmu]], [[4kn4]], [[4kn7]], [[5uac]], [[5uah]], [[5ual]], [[4zh3]], [[4zh4]] – EcSF ProD + RNAP subunits α,β,β’,ω + antibiotic <br />
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**[[4xsx]], [[4xsy]], [[4xsz]] – EcSF ProD + RNAP subunits α,β,β’,ω + antibiotic <br />
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**[[6byu]] – EcSF ProD + RNAP subunits α,β,β’,ω + ppApp <br />
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**[[4mey]], [[4ljz]], [[4lk1]], [[6cux]] – EcSF ProD + RNAP subunits α,β,β’,ω <br />
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**[[6c9y]], [[6ca0]] – EcSF ProD + RNAP subunits α,β,β’,ω - Cryo EM<br />
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**[[5byh]] – EcSF-45 + RNAP subunits α,β,β’,ω <br />
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**[[5nwt]] – EcSF-54 + RNAP subunits α,β,β’,ω <br />
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**[[5w1s]] – EcSF RpoD + RNAP subunits α,β,β’ + TraR<br />
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**[[5vsw]] – EcSF RpoD + RNAP subunits α,β,β’ + DnaK suppressor protein<br />
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**[[5w1t]] – EcSF RpoD + RNAP subunits α,β,β’ + RpoZ + DnaK suppressor protein<br />
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**[[4lk0]], [[4llg]], [[4yfk]], [[4yfn]], [[4yfx]], [[4zh2]] – EcSF ProD + EcRNAP subunits α,β,β’,ω + RNAP inhibitor<br />
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**[[4cxf]] – SF CNRH + CNRY – ''Cupriavidus metallidurans''<br />
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**[[4g6d]], [[4g8x]], [[4g94]] – SF ProD region 4 + Orf067 – ''Staphylococcus aureus''<br />
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**[[5yix]] – SF RpoD + GCRA - ''Caulobacter crescentus''<br />
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*Sigma factor complex with protein and DNA
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**[[1rio]] - TaSF region 4 + repression protein CI + DNA<br />
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**[[4oin]], [[4oip]], [[4oiq]], [[4oir]] – TtSF-A + RNAP subunits α,β,β’,ω + antibiotic + DNA<br />
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**[[4oio]], [[4g7h]], [[4g7o]], [[4g7z]], [[4q4z]], [[4q5s]] – TtSF SIGA + RNAP subunits α,β,β’,ω + DNA<br />
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**[[1smy]] – TtSF + RNAP subunits α,β,β’,ω + G4P<br />
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**[[3n97]] – TaSF region 4 + RNAP subunits α + DNA<br />
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**[[4xlp]], [[4xlq]], [[5tjg]] – TaSF SIGA + RNAP subunits α,β,β’,ω + DNA <br />
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**[[1l9u]], [[1l9z]] – TaSF + RNAP subunits α,β,β’,ω + DNA – Cryo EM <br />
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**[[4xlr]], [[4xls]] – TaSF-A + RNAP subunits α,β,β’,ω + CarD-like transcriptional regulator + DNA <br />
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**[[3iyd]] – EcSF ProD + EcRNAP subunits α,β,β’,ω + catabolite gene activator + DNA<br />
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**[[4jk1]], [[4jk2]], [[4jkr]] – EcSF ProD + EcRNAP subunits α,β,β’,ω + G4P<br />
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**[[4yln]], [[4ylo]], [[4ylp]] – EcSF ProD + EcRNAP subunits α,β,β’,ω + DNA<br />
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**[[5nss]] – EcSF-54 + EcRNAP subunits α,β,β’,ω + phage shock protein F + DNA - Cryo EM<br />
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**[[5nsr]], [[6gh6]], [[6gh5]], [[6gfw]] – EcSF-54 + EcRNAP subunits α,β,β’,ω + DNA - Cryo EM<br />
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**[[5voi]] – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA <br />
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**[[6cuu]] – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA + antibiotic<br />
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**[[5d4c]] – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA + CTP + ATP<br />
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**[[5d4d]] – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA + CTP + NAD<br />
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**[[5d4e]] – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA + CTP + dephosphate-CoA<br />
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**[[5uha]] – MtSF-A + MtRNAP subunits α,β,β’,ω + DNA <br />
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**[[6c04]] – MtSF-A + RNAP subunits α,β,β’,ω + RbpA + DNA - Cryo EM<br />
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**[[5uhe]], [[5uhf]] – MtSF SIGA + MtRNAP subunits α,β,β’,ω + DNA + inhibitor<br />
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**[[5uhg]] – MtSF-A + MtRNAP subunits α,β,β’,ω + DNA + antibiotic + inhibitor<br />
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**[[5uhb]] – MtSF-A + MtRNAP subunits α,β,β’,ω + DNA + antibiotic<br />
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**[[6bzo]] – MtSF-A + RNAP subunits α,β,β’,ω + RbpA + DNA + antibiotic - Cryo EM<br />
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**[[5tw1]], [[6cce]] – MsSF-A + MtRNAP subunits α,β,β’,ω + DNA + peptide - ''Mycobacterium smegmatis''<br />
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**[[5vi8]] – MsSF-A + MsRNAP subunits α,β,β’,ω + DNA <br />
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**[[6ccv]] – MsSF-A + MtRNAP subunits α,β,β’,ω + DNA + peptide + RbpA <br />
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**[[6ccf]] – MsSF-A + MtRNAP subunits α,β,β’,ω + DNA + peptide + antibiotic<br />
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*Sigma factor complex with protein, DNA and RNA
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**[[5vi5]] – MsSF-A + MsRNAP subunits α,β,β’,ω + RbpA + DNA + RNA<br />
 
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**[[4xln]] – TaSF-A + RNAP subunits α,β,β’,ω + DNA + RNA <br />
 
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**[[5ipl]], [[5ipm]], [[5ipn]] – EcSF RpoS + EcRNAP subunits α,β,β’,ω + DNA + RNA<br />
 
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**[[6b6h]] – EcSF RpoD + EcRNAP subunits α,β,β’,ω + DNA + RNA - Cryo EM<br />
 
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**[[5e17]], [[5e18]] – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA + RNA<br />
 
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**[[5x22]] – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA + RNA + CMPPP<br />
 
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**[[5vo8]] – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA + RNA + GTP<br />
 
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**[[5x21]] – TtSF-A + TtRNAP subunits α,β,β’,ω + DNA + RNA + antibiotic<br />
 
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**[[5i2d]] – TtSF-A + TtRNAP subunits α,β,β’,ω + transcriptional regulator + DNA + RNA<br />
 
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**[[5uh5]], [[5uh8]], [[5uh9]] – MtSF-A + MtRNAP subunits α,β,β’,ω + DNA + RNA<br />
 
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**[[5uh6]], [[5uhc]], [[5uhd]], [[5x21]] – MtSF-A + TtRNAP subunits α,β,β’,ω + DNA + RNA + antibiotic<br />
 
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}}
 
== References ==
== References ==

Current revision

Structure of sigma factor of E.Coli RNAP (grey) in complex with promoter DNA and ethylene glycol (PDB code 4lup).

Drag the structure with the mouse to rotate

References

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.


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Wally Novak, Michal Harel

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