Difference between revisions of "Promoters/Catalog"

Latest revision as of 14:39, 16 December 2019

Browse by function

	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
Constitutive(?)
Negative(?)
Multiple

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.

@@ Line 1: / Line 1: @@
-==Browse by regulation and RNA polymerase==
+==Browse by function==
 [[Image:ConstitutivePromoter.png|200px|right]]
-The registry has a large collection of [[Promoters]] available.  We categorize promoters in two ways.  First, most promoters are designed for a particular RNA polymerase (RNAP) holoenzyme, e.g ''E. coli'' RNAP bound to a particular &sigma; factor (a &sigma; factor is a protein that confers specificity on ''E. coli'' RNAP for particular promoter sequences), or the RNAP from the T7 bacteriophage.  Second, promoters are categorized by the manner in which they are regulated.  For example a promoter may be unregulated (constitutive), positively regulated (activatable) or negatively regulated (repressible).  Regulated promoters allow you to "program" biological systems.  For example, you can perform logic (e.g. "If protein X is present, promoter Y is off") or ensure that a particular gene is only expressed when a particular small molecule is present in the media.
+{|
+|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 &sigma; 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 &sigma; factor (a &sigma; 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"
@@ Line 20: / Line 40: @@
 |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|Other]]
+|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"
 |rowspan="4" width="50pt" cellpadding="0" align="center" |
@@ Line 27: / Line 47: @@
 |width="45px" align="center"|[[Image:BCInducibleIcon.png]]
 |-style="height:58px" align="right" valign="center"
-|[[Help:Promoters/Regulation|Constitutive]]
+|[[Promoters/Catalog/Constitutive|Constitutive]]([[Help:Promoters/Regulation|?]])
 |align="center"|[[Image:ConstitutiveIcon.png]]
 |-style="height:58px" align="right" valign="center"
-|[[Help:Promoters/Regulation|Negative]]
+|[[Promoters/Catalog/Negative|Negative]]([[Help:Promoters/Regulation|?]])
 |align="center"|[[Image:BCRepressibleIcon.png]]
 |-style="height:58px" align="right" valign="center"
@@ Line 38: / Line 58: @@
 |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|?]]
+|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|10]]
+|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|1]]
+|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Eukaryotic/Positive|5]]
 |-style="height:58px"
 |align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Ecoli/Constitutive|63]]
 |align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/B. subtilis/Constitutive|5]]
-|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Prokaryote/Miscellaneous/Constitutive|?]]
+|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Prokaryote/Miscellaneous/Constitutive|2]]
 |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|2]]
+|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Eukaryotic/Constitutive|11]]
 |-style="height:58px"
 |align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;"|[[Promoters/Catalog/Ecoli/Repressible|89]]
 |align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/B. subtilis/Repressible|1]]
-|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Prokaryote/Miscellaneous/Negative|?]]
+|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Prokaryote/Miscellaneous/Negative|-]]
 |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|2]]
+|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"
 |align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Ecoli/Multiple|111]]
 |align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Subtilis/Multiple|-]]
-|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Prokaryote/Miscellaneous/Multiple|?]]
+|align="center" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |[[Promoters/Catalog/Prokaryote/Miscellaneous/Multiple|1]]
 |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|1]]
+|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]]
 |-
@@ Line 71: / Line 91: @@
 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.
-==Browse by Family==
-Within the registry collection of promoters, there are also some smaller collections consisting of promoters that are all closely related or that have all been characterized in a similar manner.  You can browse these collections below.
-*[[Promoters/Catalog/Anderson|'''Anderson Promoter Collection''']] - a well-characterized collection of ''E. coli'' &sigma;<sup>70</sup> constitutive promoters contributed to the registry by Chris Anderson.
-*[[Promoters/Catalog/USTC|'''USTC Promoter Collection''']] - a collection of multiple input promoters all based on a similar template.  These promoters were developed by the 2007 USTC iGEM team.
-*[[Promoters/Catalog/Madras|'''IIT Madras Promoter Collection''']] - a well-characterized collection of negatively regulated ''E. coli'' promoters that have been engineered to be recognized by alternative &sigma; factors.  This collection was developed by the 2008 IIT Madras iGEM team.
-*[[Promoters/Catalog/T7|'''T7 Promoters''']] - a collection of all T7 promoters available from the registry.  The promoters are often used for very high expression of a protein.  These promoters work in ''E. coli'' but require T7 RNAP to be present.