Libraries of Modules in Synthetic Biology

In a Synthetic biology scenario modules can describe the molecular interactions involved in a well characterised synthetic construct as a Biobrick that can be reused in the development of different synthetic cellular designs. For example, the following library illustrates how two different inverters can be designed in an incremental manner and introduced in a library in order to facilitate their inclusion in different synthetic cellular designs:

libraryOfModules inverters

      PostTransc({X},{c_1,c_2,c_3,c_4,c_5},{l}) =
      {
          r1: [ rnaX_RNAP ]_l -c_1-> [ rnaX ]_l
          r2: [ rnaX ]_l -c_2-> [ ]_l
          r3: [ rnaX ]_l -c_3-> [ rnaX + proteinX_Rib ]_l
          r4: [ proteinX_Rib ]_l -c_4-> [ proteinX ]_l
          r5: [ proteinX ]_l -c_5-> [ ]_l
      }

      Plac({X},{c_1,c_2,c_3,c_4},{l}) =
      {
          r1: [ Plac_geneX ]_l -c_1-> [ Plac_geneX + rnaX_RNAP ]_l
          r2: [ proteinLacI + Plac_geneX ]_l -c_2-> [ Plac_LacI_geneX ]_l
          r3: [ Plac_LacI_geneX ]_l -c_3-> [ proteinLacI + Plac_geneX ]_l
          r4: [ IPTG + Plac_LacI_geneX ]_l -c_4-> [ proteinLacI_IPTG + Plac_geneX ]_l
      }

      PR({X},{c_1,c_2,c_3,c_4,c_5},{l}) =
      {
          r1: [ PR_geneX ]_l -c_1-> [ PR_geneX + rnaX_RNAP ]_l
          r2: [ proteinCI2 + PR_geneX ]_l -c_2-> [ PR_CI2_geneX ]_l
          r3: [ PR_CI2_geneX ]_l -c_3-> [ proteinCI2 + PR_geneX ]_l
          r4: [ proteinCI2 + PR_CI2_geneX ]_l -c_4-> [ PR_CI4_geneX ]_l
          r5: [ PR_CI4_geneX ]_l -c_5-> [ proteinCI2 + PR_CI2_geneX ]_l
      }

      Inverter_LacI({X},{},{l}) =
      {
          PostTransc({LacI},{},{l}) from this
          Plac({X}{}{l}) from this
      }

      Inverter_CI({X},{},{l}) =
      {
          PostTransc({CI},{},{l}) from this
          PR({X}{}{l}) from this
      }

endLibraryOfModules

The inverters library consists of five modules:

• The PostTransc module describes transcription elongation and termination (r1), RNA degradation (r2), translation initiation (r3), translation elongation and termination (r4) and protein degradation (5) . This module can be seen as having the object rnaX_RNAP as input and the object proteinX as output. The string-object rnaX_RNAP represents an RNA polymerase that has initiated transcription of the geneX and proteinX represents the protein product of geneX.

BioBrick representation of our PostTransc module.

• The Plac module describes the binding and debinding (r2 and r3) of the repressor proteinLacI to and from the lactose operon promoter. This repressor prevents the initiation of the transcription of the gene fused to the promoter represented as the production of the string-object rnaX_RNAP (r1). This module also considers the case when the repressor debinds from the promoter in the presence of the signal IPTG (r4). This module can be considered to have the repressor proteinLacI and signal IPTG as input and rnaX_RNAP as output.

BioBrick representation of our Plac module.

• The PR module describes the cooperative binding and debinding (rules r2 - r5) of the repressor CI to the PR promoter of the bacteriophage lambda. This repressor prevents the initiation of the transcription of the gene fused to the promoter represented as the production of the string-object rnaX_RNAP (r1). This module can be considered to have the repressor proteinCI as input and rnaX_RNAP as output.

BioBrick representation of our PR module.

• The Inverter_LacI module uses the repressor LacI and the promoter Plac to construct a molecular inverter with input transcripts of the LacI gene, rnaLacI_RNAP, and output transcripts of the gene fused to the promoter Plac, rnaX_RNAP. This is achieved by composing the module PostTransc instantiated with LacI and its characteristic rates and the module Plac.

BioBrick representation of the inverter using the LacI repressor.

• The Inverter_CI module uses the repressor CI and the promoter PR to construct a molecular inverter with input transcripts of the CI gene, rnaCI_RNAP, and output transcripts of the gene fused to the promoter PR, rnaX_RNAP. This is achieved by composing the module PostTransc instantiated with CI and its characteristic rates and the module PR.

BioBrick representation of the inverter using the CI repressor.