Difference between revisions of "Promoters/Catalog"
(→‎Browse by regulation and RNA polymerase)
 
(59 intermediate revisions by 4 users not shown)
Line 1: Line 1:
−
The registry has a large collection of [[Promoters]] available.  We categorize promoters using two different parameters.  First, most promoters are designed for a particular RNA polymerase holoenzyme, e.g ''E. coli'' RNA polymerase with σ70, or T7 RNA polymerase. Second, promoters may be either unregulated (constitutive), positively regulated (inducible) or negatively regulated (repressible).  So for example, if you want express a gene in growing ''E. coli'' at a with little expression before hand, you might choose a lacI repressible σ70 promoter.  
+
==Browse by function==
 +
[[Image:ConstitutivePromoter.png|200px|right]]
 +
{|
 +
|align='center' width=80px |{{Click || image=ConstitutivePromoterButton.png | link=Promoters/Catalog/Constitutive |width=48px | height=48px }}
 +
|'''[[Promoters/Catalog/Constitutive|Constitutive promoters]]''': These promoters are active independent of transcription factors, and are "on" by default.
 +
|-
 +
|align='center' width=80px |{{Click || image=Cellsignalling.png | link=Promoters/Catalog/Cell Signalling |width=48px | height=48px }}
 +
|'''[[Promoters/Catalog/Cell signalling|Cell signalling]]''': The registry has a set of promoters related to sending and receiving signals between different cells.
 +
|-
 +
|align='center' width=80px |{{Click || image=MetalButton.png | link=Promoters/Catalog/Metal sensitive |width=48px | height=48px }}
 +
|'''[[Promoters/Catalog/Metal sensitive |Metal sensitive]]''': This set includes promoters that are sensitive to various metals.  The promoters are typically regulated by a receptor protein that binds to the metal ion or complex.
 +
|-
 +
|align='center' width=80px |{{Click || image=PhageButton.png | link=Promoters/Catalog/Phage |width=48px | height=48px }}
 +
|'''[[Promoters/Catalog/Phage |Phage promoters]]''': A collection of all phage promoters available from the registry.  The promoters are often used for very high expression of a protein. These promoters work in ''E. coli'' and other chassis but typically require a particular RNA polymerase to be present.
 +
|-
 +
|align='center' width=80px |{{Click || image= StressKitButton.png | link=Promoters/Catalog/Madras |width=48px | height=48px}}
 +
|'''[[Promoters/Catalog/Madras |IIT Madras Stresskit promoters]]''': a well-characterized collection of negatively regulated ''E. coli'' promoters that have been engineered to be recognized by alternative σ factors.  This collection was developed by the 2008 IIT Madras iGEM team.
 +
|-
 +
|align='center' width=80px |{{Click || image= LogicButton.png | link=Promoters/Catalog/USTC |width=48px | height=48px}}
 +
|'''[[Promoters/Catalog/USTC |USTC logic promoters]]''': a collection of multiple input promoters all based on a similar template.  These promoters were developed by the 2007 USTC iGEM team.
 +
|-
 +
|}
  
−
The value of the parts in this catalog increases the more you use them and report your results so please remember to contribute back any data (positive or negative!) that you obtain for any promoters in the catalog.
+
==Browse by regulation and RNA polymerase==
 +
Most promoters are designed for a particular RNA polymerase (RNAP) holoenzyme, e.g ''E. coli'' RNAP bound to a particular σ factor (a σ factor is a protein that confers specificity on ''E. coli'' RNAP for particular promoter sequences), or the RNAP from the T7 bacteriophage.  Promoters are also categorized by the manner in which they are regulated.  For example, a promoter can be unregulated (constitutive), positively regulated (activatable) or negatively regulated (repressible).
  
−
 
+
{|border="0" cellpadding="0" cellspacing="0" style="margin: 1em 1em 1em 0; border-collapse: collapse;" align="center"  
−
{|align="center" border="1" cellpadding="0" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" width="100%"
+
!rowspan="2" width="130px" |
−
!colspan="2" rowspan="3"|Regulation
+
!colspan="7" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|RNA Polymerase
−
!colspan="3"|RNA Polymerase
+
 
|-
 
|-
−
|align="center" colspan="2"|[[Help:Promoters/E.coli RNAP|''E. coli'']]
+
|align="center" colspan="3" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Help:Promoters/Prokaryotic RNAP|''Prokaryotic'']]
−
|align="center"|[[Help:Promoters/T7RNAP|T7]]
+
|align="center" colspan="2" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Help:Promoters/Bacteriophage RNAP|Bacteriophage]]
 +
|align="center" colspan="2" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Help:Promoters/Eukaryotic RNAP|Eukaryotic]]
 
|-
 
|-
−
|align="center"|[[Help:Promoters/Sigma70|&sigma;<sup>70</sup>]]
+
|align="center" colspan="1" style="border:#FFFFFF 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|'''Regulation'''
−
|align="center"|[[Help:Promoters/SigmaS|&sigma;<sup>S</sup>]]
+
|align="center" width = "80" colspan="1" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Help:Promoters/Prokaryotic RNAP#E. coli RNA polymerases|''E. coli'']]
−
|
+
|align="center" width = "80"  colspan="1" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Help:Promoters/Prokaryotic RNAP#B. subtilis RNA polymerases |''B. subtilis'']]
 +
|align="center" width = "80" colspan="1" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Help:Promoters/Prokaryotic RNAP|Miscellaneous prokaryotic]]
 +
|align="center" width = "80" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Help:Promoters/Bacteriophage RNAP|T7]]
 +
|align="center" width = "80" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Help:Promoters/Bacteriophage RNAP|SP6]]
 +
|align="center" width = "80" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Help:Promoters/Eukaryotic RNAP |Yeast]]
 +
|align="center" width = "80" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Help:Promoters/Eukaryotic RNAP|Miscellaneous eukaryotic]]
 
|-style="height:58px"  
 
|-style="height:58px"  
−
|rowspan="4" width="50pt" align="center" |[[Image:BCInducibleIcon.png]][[Image:ConstitutiveIcon.png]][[Image:BCRepressibleIcon.png]][[Image:BCMultipleIcon.png]]
+
|rowspan="4" width="50pt" cellpadding="0" align="center" |
−
|width="50pt" |Inducible
+
{|cellpadding="0" cellspacing="0" align="right"
−
|align="center"| See X promoters
+
| valign="center" style="height:58px" align="right" width="80px"|[[Help:Promoters/Regulation|Positive]]
−
|align="center"| See X promoters
+
|width="45px" align="center"|[[Image:BCInducibleIcon.png]]
−
|align="center"| See X promoters
+
|-style="height:58px" align="right" valign="center"
 +
|[[Promoters/Catalog/Constitutive|Constitutive]]([[Help:Promoters/Regulation|?]]) 
 +
|align="center"|[[Image:ConstitutiveIcon.png]]
 +
|-style="height:58px" align="right" valign="center"
 +
|[[Promoters/Catalog/Negative|Negative]]([[Help:Promoters/Regulation|?]]) 
 +
|align="center"|[[Image:BCRepressibleIcon.png]]
 +
|-style="height:58px" align="right" valign="center"
 +
|[[Help:Promoters/Regulation|Multiple]]
 +
|align="center"|[[Image:BCMultipleIcon.png]]
 +
|}
 +
|align="center" cellspacing="1" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Ecoli/Positive|53]]
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/B. subtilis/Positive|1]]
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Prokaryote/Miscellaneous/Positive|6]]
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |-
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |-
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Yeast/Positive|14]]
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Eukaryotic/Positive|5]]
 
|-style="height:58px"  
 
|-style="height:58px"  
−
|Constitutive
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Ecoli/Constitutive|63]]
−
|align="center"| See X promoters
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/B. subtilis/Constitutive|5]]
−
|align="center"| See X promoters
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Prokaryote/Miscellaneous/Constitutive|2]]
−
|align="center"| See X promoters
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/T7/Constitutive|12]]
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/SP6/Constitutive|1]]
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Yeast/Constitutive|10]]
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Eukaryotic/Constitutive|11]]
 
|-style="height:58px"  
 
|-style="height:58px"  
−
|Repressible
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Promoters/Catalog/Ecoli/Repressible|89]]
−
|align="center"| See X promoters
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/B. subtilis/Repressible|1]]
−
|align="center"| See X promoters
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Prokaryote/Miscellaneous/Negative|-]]
−
|align="center"| See X promoters
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/T7/Repressible|6]]
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |-
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Yeast/Repressible|3]]
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Eukaryotic/Repressible|7]]
 
|-style="height:38px"  
 
|-style="height:38px"  
−
|Multiple
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Ecoli/Multiple|111]]
−
|align="center"| See X promoters
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Subtilis/Multiple|-]]
−
|align="center"| See X promoters
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Prokaryote/Miscellaneous/Multiple|1]]
−
|align="center"| See X promoters
+
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |-
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |-
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Yeast/Multiple|5]]
 +
|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Eukaryotic/Multiple|4]]
 
|-
 
|-
 
|}
 
|}
 +
 +
We also have a collection of [[Promoters/Catalog/Miscellaneous|miscellaneous promoters]] available that are provided "as is".  If you can contribute more information about these promoters, for example, by providing the information that will allow us to add them into one of the categories in the table above, please do so.

Latest revision as of 14:39, 16 December 2019

Browse by function

ConstitutivePromoter.png
Constitutive promoters: These promoters are active independent of transcription factors, and are "on" by default.
Cell signalling: The registry has a set of promoters related to sending and receiving signals between different cells.
Metal sensitive: This set includes promoters that are sensitive to various metals. The promoters are typically regulated by a receptor protein that binds to the metal ion or complex.
Phage promoters: A collection of all phage promoters available from the registry. The promoters are often used for very high expression of a protein. These promoters work in E. coli and other chassis but typically require a particular RNA polymerase to be present.
IIT Madras Stresskit promoters: a well-characterized collection of negatively regulated E. coli promoters that have been engineered to be recognized by alternative σ factors. This collection was developed by the 2008 IIT Madras iGEM team.
USTC logic promoters: a collection of multiple input promoters all based on a similar template. These promoters were developed by the 2007 USTC iGEM team.

Browse by regulation and RNA polymerase

Most promoters are designed for a particular RNA polymerase (RNAP) holoenzyme, e.g E. coli RNAP bound to a particular σ factor (a σ factor is a protein that confers specificity on E. coli RNAP for particular promoter sequences), or the RNAP from the T7 bacteriophage. Promoters are also categorized by the manner in which they are regulated. For example, a promoter can be unregulated (constitutive), positively regulated (activatable) or negatively regulated (repressible).

RNA Polymerase
Prokaryotic Bacteriophage Eukaryotic
Regulation E. coli B. subtilis Miscellaneous prokaryotic T7 SP6 Yeast Miscellaneous eukaryotic
Positive BCInducibleIcon.png
Constitutive(?) ConstitutiveIcon.png
Negative(?) BCRepressibleIcon.png
Multiple BCMultipleIcon.png
53 1 6 - - 14 5
63 5 2 12 1 10 11
89 1 - 6 - 3 7
111 - 1 - - 5 4

We also have a collection of miscellaneous promoters available that are provided "as is". If you can contribute more information about these promoters, for example, by providing the information that will allow us to add them into one of the categories in the table above, please do so.