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

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Activated Promoter RBS coupled Architecture

  • Description: Promoter coupled to RBS to provide a synthesis rate of protein depending on the amount of activator
  • Hypothesis:
    • Constant and continuous transcription and translation rate
    • Maximum synthesis rate depends on number of gene copies
    • quasi steady state approx on mRNA
    • unlimited resources for transcription and translation (excess in polymerase ...)
    • Binding of the activator on the promoter (Hill-function-type equation)
  • Inputs:
    • activator
    • nb-gene-copies
  • Outputs:
    • Synthesis rate
  • Characteristic parameters:
    • max-transcription-rate-per-gene
    • K (dissociation-constant)
    • n (Hill-coefficient)
Activated Promoter/RBS Brick Architecture
Activated Promoter/RBS Brick Architecture

CellML structure (CellML 1.1 spec)

  • Component: ActivatedPromoterRBSCoupled
  • Units:
    • Imported from Environment component
  • Variables:
    • nbGeneCopies (public interface = in / init value = 1.0)
    • maxSynthesisRate (public interface = none / init value = XXX)
    • K (dissociation constant) (public interface = none / init value = XXX)
    • n (Hill coefficient) (public interface = none / init value = XXX)
    • synthesisRate (public interface = out / init value = XXX)
    • activator (public interface = in )
  • MathML
    • amsmath


CellML File

<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="file:///C:/CellML_models/promoter-RBS_activated.cml"
      cmeta:id="promoter-RBS_activated"
      name="promoter-RBS_activated">
 


<component name="promoter-RBS_activated">

   <variable name="synthesisRate"                initial_value=""    public_interface="out"  units="moles_per_second"/>
   <variable name="synthesisRatePerGene"         initial_value="1"   public_interface="none" units="moles_per_second"/>
   <variable name="activatorConcentration"       initial_value="0"   public_interface="in"   units="mole"/>
   <variable name="nb_gene"                      initial_value="1"   public_interface="none" units="dimensionless"/>
   <variable name="dissociation_constant"        initial_value="1"   public_interface="none" units="dimensionless"/>
   <variable name="hill_coefficient"             initial_value="2"   public_interface="none" units="dimensionless"/>

Failed to parse (Missing texvc executable; please see math/README to configure.): <apply id="synthesisRate"> <eq/> <ci>synthesisRate</ci> <apply> <divide/> <apply> <times/> <ci>synthesisRatePerGene</ci> <ci>nb_gene</ci> <ci>activatorConcentration</ci> </apply> <apply> <plus/> <apply> <power/> <ci>dissociation_constant</ci> <ci>hill_coefficient</ci> </apply> <apply> <power/> <ci>activatorConcentration</ci> <ci>hill_coefficient</ci> </apply> </apply> </apply> </apply>


</component>



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

       xlink:href="file://C:\CellML_models\units.cml">
     <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 and a given level of the activator
  • To characterize this part you need to get {maxSynthesisRate} and {sensitivity}. It can be achieved experimentally using a quantitative GFP assay. Measurement of GFP levels should be done at steady state with different levels of the activator.
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