Registry of Standard Biological Models/Basic Component Models/Promoter RBS Coupled

Promoter RBS Coupled Architecture

Description: Promoter coupled to RBS to provide a constitutive synthesis rate of protein Hypothesis: Constant and continuous transcription and translation rate Synthesis rate depends on number of gene copies quasi steady state approx applied on mRNA population unlimited resources for transcription and translation (excess in polymerase, ribosomes, tRNAs...) Inputs: nbGeneCopies (from a Plasmid modules for example) Outputs: RiPSOut (Ribosomes Per Second OUT - see RiPS definition) Characteristic parameters: RiPSOutPerGene

Constitutive Promoter/RBS Brick Architecture (To be Updated)

CellML structure (CellML 1.1 spec)

• Component: PromoterRBSCoupled
• Units:
  • Imported from Environment component
• Variables:
  • nbGeneCopies (public interface = in / init value = 1.0)
  • RiPSOutPerGene (public interface = none / init value = XXX)
  • RiPSOut (public interface = out / init value = depends on the promoter-RBS used)
• MathML
  • [math]\displaystyle{ RiPSOut = nbGeneCopies*RiPSOutPerGene }[/math]

Examples

BioBricks from Registry	CellML file
<bbpart>BBa_J13211</bbpart> ==> TetR (<bbpart>BBa_R0040</bbpart>) + RBS (<bbpart>BBa_R0032</bbpart>)	Media:BBa_J13211_Model.xml
other part	other file

CellML File

CellML Code

<syntax type = 'xml'>

<?xml version="1.0"?>

<model xmlns="http://www.cellml.org/cellml/1.0#"

      xmlns:cmeta="http://www.cellml.org/metadata/1.0#" 
      xml:base="http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/Promoter_RBS_Coupled/CellML_Code&action=raw"
      cmeta:id="promoter-RBS_constitutive"
      name="promoter-RBS_constitutive">
 

<component name="promoter-RBS_constitutive">

<variable name="RiPSOut" initial_value="" public_interface="out" units="moles_per_second"/> <variable name="nbGeneCopies" initial_value="1" public_interface="none" units="dimensionless"/> <variable name="RiPSOutPerGene" initial_value="1" public_interface="none" units="moles_per_second"/>

[math]\displaystyle{ \lt apply id="RiPSOut"\gt \lt eq/\gt \lt ci\gt RiPSOut\lt /ci\gt \lt apply\gt \lt times/\gt \lt ci\gt RiPSOutPerGene\lt /ci\gt \lt ci\gt nbGeneCopies\lt /ci\gt \lt /apply\gt \lt /apply\gt }[/math]

</component>

<import xmlns:xlink="http://www.w3.org/1999/xlink"

             xlink:href="http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/Units&action=raw">

     <units name="moles_per_second" units_ref="moles_per_second"/>
     <units name="per_second"       units_ref="per_second"/>

</import>

</model> </syntax>

Comments

• This component is simply a container providing the synthesis rate specific to a constitutive promoter coupled to a RBS
• Having a model of a promoter and RBS coupled could mean that we have a constant synthesis rate of the downstream protein(s) (quasi steady state approx)
• This parameter is easier to characterize experimentally. Using a calibrated GFP assay with none half-life, we know that at steady state (synthesis = degradation)