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

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Contents

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:
  • Characteristic parameters:
    • RiPSOutPerGene
Constitutive Promoter/RBS Brick Architecture (To be Updated)
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
    • RiPSOut = nbGeneCopies * RiPSOutPerGene

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"/>

Failed to parse (lexing error): <apply id="RiPSOut"> <eq/> <ci>RiPSOut</ci> <apply> <times/> <ci>RiPSOutPerGene</ci> <ci>nbGeneCopies</ci> </apply> </apply>


</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)
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