Difference between revisions of "Help:Regulatory"
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[[Category:Regulatory]]
 
[[Image:Part icon regulatory.png]]
 
[[Image:Part icon regulatory.png]]
 
<small>Browse [https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Regulatory Regulatory] parts!</small><br>
 
<small>Browse [https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Regulatory Regulatory] parts!</small><br>
 
<hr>
 
<hr>
  
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Regulatory parts are those which provide binding regions for RNA polymerase, the enzyme which performs the act of <b>transcription</b> (the conversion of DNA to RNA).<br>
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Regulatory parts (also known as ''promoters'') are those which provide binding regions for RNA polymerase, the enzyme which performs the act of <b>transcription</b> (the conversion of DNA to RNA).
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E.coli's RNA polymerase is a large enzyme which spans about 6 turns of a DNA helix, which is equivalent to about 60 base pairs.  Thus most promoter regions for e.coli are approximately 60 bp in length.
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E.coli's RNA polymerase is a large enzyme which spans about 6 turns of a DNA helix, which is equivalent to about 60 base pairs.  Thus many promoter regions for e.coli are approximately 60 bp in length.
  
 
Some sub-categories of Regulatory parts are:<br>
 
Some sub-categories of Regulatory parts are:<br>
  
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==Constitutive parts==
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==Control==
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Parts which allow for continual transcription of parts. Often these parts can be de-activated (transcription downregulated) by the addition of ligand.  The use of constituitive promoters can be desirable since they are less susceptible to cross-talk and can hypothetically take in [[PoPS]] input.   
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This describes whether the default state of the regulatory region is normally in the:
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* 'on' (<b>[https://parts.igem.org/wiki/index.php?title=Help:Regulatory&action=edit#Repressible repressible]</b>) or
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* 'off' (<b>[https://parts.igem.org/wiki/index.php?title=Help:Regulatory&action=edit#Inducible_parts inducible]</b>) state of transcription.  Note that "normally" denotes a system in a static state with no inputs provided (ie. if this were the only Biobrick to exist on the only plasmid in a cell strain).  <br>
  
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Examples of constitutive parts include  
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<small>Please note: ligands associated with specific cell strains may cause changes in the control behaviour of the part.  These changes should be noted on the [https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Regulatory regulatory parts] or [https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=cell cell strain page].  </small><br>
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===Repressible===
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Regulatory regions which allow for continual high-level transcription of DNA.  Often these parts can be down-regulated (transcription downregulated) by the addition of ligand.  The use of constituitive promoters can be desirable since they are less susceptible to cross-talk and can hypothetically take in [[Help:PoPS|PoPS]] input. 
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{|border="1" style="background:#CCFFCC;"
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|
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Examples of repressible parts include
 
*[[Part:BBa_R0040]] - the pTet promoter region, controlled by tetracycline or its chemical analog [http://openwetware.org/wiki/ATc ATC]
 
*[[Part:BBa_R0040]] - the pTet promoter region, controlled by tetracycline or its chemical analog [http://openwetware.org/wiki/ATc ATC]
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*[[Part:BBa_R0010]] - the pLac promoter region, controlled by the lactose protein or by its chemical analog [http://openwetware.org/wiki/IPTG IPTG]
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*[[Part:BBa_R0011]] - the pLac promoter region, controlled by the disaccharide sugar lactose or by its chemical analog [http://openwetware.org/wiki/IPTG IPTG]
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*[[Part:BBa_R0051]] - the pR bacteriophage lambda promoter region, controlled by the presence of the cI protein
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|}
  
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==Inducible parts==
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Parts which are continually "off" (transcription is not induced), but allow for activation (increase transcription) through the addition of particular chemicals <br>
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===Inducible parts===
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Parts which are continually "off" (at low DNA transcription levels), but allow for activation (increased transcription) through the addition of particular ligands <br>
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{|border="1" style="background:#CCFFCC;"
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|
 
Examples include:
 
Examples include:
 
*[[Part:BBa_R0080]] - The araC promoter region, which can be activated by the addition of the sugar [http://openwetware.org/wiki/Arabinose arabinose]
 
*[[Part:BBa_R0080]] - The araC promoter region, which can be activated by the addition of the sugar [http://openwetware.org/wiki/Arabinose arabinose]
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*[[Part:BBa_I0500]] - Another [http://openwetware.org/wiki/Arabinose arabinose] inducible promoter region
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|}
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===Other parts===
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These are parts which can be either upregulated or downregulated in their normal state
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==Engineering systems using Regulatory Parts==
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Often system control ligands are proteins or small molecules developed within the cell.  Due to their degradation outside of the cell, most endogenously manufactured control ligands are hard to regulate closely and thus not ideal for engineering systems. 
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However, there are some ligand molecules which are not subject to degradation, and thus are useful for adding to a system
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{|border="1" style="background:#CCCCFF;"
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|
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Examples include:
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*[http://openwetware.org/wiki/Arabinose arabinose]: A simple sugar which can induce the Pbad promoter region.  One such biobrick is [[Part:BBa_I0500]].
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*[http://openwetware.org/wiki/ATc ATc]: anhydrotetracycline (ATc) is a tetracycline analog, showing increased (30x) affinity for tet repressor.
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*[http://openwetware.org/wiki/IPTG IPTG]: Isopropyl-beta-D-thiogalactopyranoside (IPTG) Induces transcription from promoters regulated by lacI repressor.
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|}
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==Direction==
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A regulatory region can point RNA polymerase in either the ''forward'' or ''reverse'' directions depending on which strand of the double stranded DNA molecule it decides to bind to.  Currently most Biobrick regulatory parts transcribe DNA in the forward direction.<br>
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<br>
  
 
==References==
 
==References==
 
# Ptashne, Mark.  "A Genetic Switch".  Cold Spring Harbor Press, 1986.
 
# Ptashne, Mark.  "A Genetic Switch".  Cold Spring Harbor Press, 1986.

Latest revision as of 21:48, 20 July 2017

Part icon regulatory.png Browse Regulatory parts!

Regulatory parts (also known as promoters) are those which provide binding regions for RNA polymerase, the enzyme which performs the act of transcription (the conversion of DNA to RNA).

E.coli's RNA polymerase is a large enzyme which spans about 6 turns of a DNA helix, which is equivalent to about 60 base pairs. Thus many promoter regions for e.coli are approximately 60 bp in length.

Some sub-categories of Regulatory parts are:

Control

This describes whether the default state of the regulatory region is normally in the:

  • 'on' (repressible) or
  • 'off' (inducible) state of transcription. Note that "normally" denotes a system in a static state with no inputs provided (ie. if this were the only Biobrick to exist on the only plasmid in a cell strain).

Please note: ligands associated with specific cell strains may cause changes in the control behaviour of the part. These changes should be noted on the regulatory parts or cell strain page.

Repressible

Regulatory regions which allow for continual high-level transcription of DNA. Often these parts can be down-regulated (transcription downregulated) by the addition of ligand. The use of constituitive promoters can be desirable since they are less susceptible to cross-talk and can hypothetically take in PoPS input.

Examples of repressible parts include

  • Part:BBa_R0040 - the pTet promoter region, controlled by tetracycline or its chemical analog [http://openwetware.org/wiki/ATc ATC]
  • Part:BBa_R0011 - the pLac promoter region, controlled by the disaccharide sugar lactose or by its chemical analog [http://openwetware.org/wiki/IPTG IPTG]


Inducible parts

Parts which are continually "off" (at low DNA transcription levels), but allow for activation (increased transcription) through the addition of particular ligands

Examples include:

  • Part:BBa_R0080 - The araC promoter region, which can be activated by the addition of the sugar [http://openwetware.org/wiki/Arabinose arabinose]

Other parts

These are parts which can be either upregulated or downregulated in their normal state

Engineering systems using Regulatory Parts

Often system control ligands are proteins or small molecules developed within the cell. Due to their degradation outside of the cell, most endogenously manufactured control ligands are hard to regulate closely and thus not ideal for engineering systems.

However, there are some ligand molecules which are not subject to degradation, and thus are useful for adding to a system

Examples include:

  • [http://openwetware.org/wiki/Arabinose arabinose]: A simple sugar which can induce the Pbad promoter region. One such biobrick is Part:BBa_I0500.
  • [http://openwetware.org/wiki/ATc ATc]: anhydrotetracycline (ATc) is a tetracycline analog, showing increased (30x) affinity for tet repressor.
  • [http://openwetware.org/wiki/IPTG IPTG]: Isopropyl-beta-D-thiogalactopyranoside (IPTG) Induces transcription from promoters regulated by lacI repressor.


Direction

A regulatory region can point RNA polymerase in either the forward or reverse directions depending on which strand of the double stranded DNA molecule it decides to bind to. Currently most Biobrick regulatory parts transcribe DNA in the forward direction.

References

  1. Ptashne, Mark. "A Genetic Switch". Cold Spring Harbor Press, 1986.