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

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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)

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]


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=""


<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]


<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
  • 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)