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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. | | '''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 /> |
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| == 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>
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| ==3D structures of sigma factor== | | ==3D structures of sigma factor== |
| | [[Sigma factor 3D structures]] |
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| Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
| | </StructureSection> |
| {{#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 SIGR region 4<br />
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| **[[5mww]] – BsSF SIGA region 1.1 - ''Bacillus subtilis'' - NMR <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 + membrane protein – ''Mycobacterium tuberculosis''<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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| **[[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 SIGA + RNAP subunits α,β,β’,ω + protein + G4P<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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| **[[4mey]], [[4ljz]], [[4lk1]] – EcSF ProD + RNAP subunits α,β,β’,ω <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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| *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 SIGA + 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]] – EcSF-54 + EcRNAP subunits α,β,β’,ω + DNA - Cryo EM<br />
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| **[[5voi]] – TtSF SIGA + TtRNAP subunits α,β,β’,ω + DNA <br />
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| **[[5d4c]] – TtSF SIGA + TtRNAP subunits α,β,β’,ω + DNA + CTP + ATP<br />
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| **[[5d4d]] – TtSF SIGA + TtRNAP subunits α,β,β’,ω + DNA + CTP + NAD<br />
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| **[[5d4e]] – TtSF SIGA + TtRNAP subunits α,β,β’,ω + DNA + CTP + dephosphate-CoA<br />
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| **[[5uha]] – MtSF SIGA + MtRNAP subunits α,β,β’,ω + DNA <br />
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| **[[5uhe]], [[5uhf]] – MtSF SIGA + MtRNAP subunits α,β,β’,ω + DNA + inhibitor<br />
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| **[[5uhg]] – MtSF SIGA + MtRNAP subunits α,β,β’,ω + DNA + antibiotic + inhibitor<br />
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| **[[5uhb]] – MtSF SIGA + MtRNAP subunits α,β,β’,ω + DNA + antibiotic<br />
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| **[[5tw1]] – MsSF SIGA + MtRNAP subunits α,β,β’,ω + DNA + peptide - ''Mycobacterium smegmatis''<br />
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| **[[5vi8]] – MsSF SIGA + MsRNAP subunits α,β,β’,ω + DNA <br />
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| *Sigma factor complex with protein, DNA and RNA
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| **[[5vi5]] – MsSF SIGA + MsRNAP subunits α,β,β’,ω + RbpA + DNA + RNA<br />
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| **[[4xln]] – TaSF SIGA + 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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| **[[5e17]], [[5e18]] – TtSF SIGA + TtRNAP subunits α,β,β’,ω + DNA + RNA<br />
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| **[[5x22]] – TtSF SIGA + TtRNAP subunits α,β,β’,ω + DNA + RNA + CMPPP<br />
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| **[[5vo8]] – TtSF SIGA + TtRNAP subunits α,β,β’,ω + DNA + RNA + GTP<br />
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| **[[5i2d]] – TtSF SIGA + TtRNAP subunits α,β,β’,ω + transcriptional regulator + DNA + RNA<br />
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| **[[5uh5]], [[5uh8]], [[5uh9]] – MtSF SIGA + MtRNAP subunits α,β,β’,ω + DNA + RNA<br />
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| **[[5uh6]], [[5uhc]], [[5uhd]], [[5x21]] – MtSF SIGA + TtRNAP subunits α,β,β’,ω + DNA + RNA + antibiotic<br />
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| }}
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| == References == | | == References == |
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