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

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>synthesisRate = \frac{nbGeneCopies*maxSynthesisRate*[activator]^{n}}{K^{n}+[activator]^{n}} </amsmath>

CellML File

<syntax type='xml'>

<?xml version="1.0"?>

<model xmlns=""


<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"/>

[math]\displaystyle{ \lt apply id="synthesisRate"\gt \lt eq/\gt \lt ci\gt synthesisRate\lt /ci\gt \lt apply\gt \lt divide/\gt \lt apply\gt \lt times/\gt \lt ci\gt synthesisRatePerGene\lt /ci\gt \lt ci\gt nb_gene\lt /ci\gt \lt ci\gt activatorConcentration\lt /ci\gt \lt /apply\gt \lt apply\gt \lt plus/\gt \lt apply\gt \lt power/\gt \lt ci\gt dissociation_constant\lt /ci\gt \lt ci\gt hill_coefficient\lt /ci\gt \lt /apply\gt \lt apply\gt \lt power/\gt \lt ci\gt activatorConcentration\lt /ci\gt \lt ci\gt hill_coefficient\lt /ci\gt \lt /apply\gt \lt /apply\gt \lt /apply\gt \lt /apply\gt }[/math]


<import xmlns:xlink=""

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


</model> </syntax>


  • 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.