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

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="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"/>

[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]

</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.