Team:Bielefeld-Germany/Data Page

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This page gives a basic overview about our cellfree Bisphenol A biosensor system and the BioBricks we have used. A more detailed description of the biosensor system can be found in our [[Team:Bielefeld-Germany/Project/Description | project description]] and in the [[Team:Bielefeld-Germany/Project/Background/BPA | Bisphenol A]], [[Team:Bielefeld-Germany/Project/Background/S-Layer | S-Layer]] and [[Team:Bielefeld-Germany/Project/Background/NDA | NAD<sup>+</sup> detection]] background sections.
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This page gives a basic overview about our cell-free bisphenol A biosensor system and the BioBricks we have used. A more detailed description of the biosensor system can be found in our [[Team:Bielefeld-Germany/Project/Description | project description]] as well as in the [[Team:Bielefeld-Germany/Project/Background/BPA | bisphenol A]], [[Team:Bielefeld-Germany/Project/Background/S-Layer | S-layer]] and [[Team:Bielefeld-Germany/Project/Background/NAD | NAD<sup>+</sup> detection]] background subsections.  
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==How our System works==
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==How our system works==
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[[Image:Bielefeld_2011_S-Layer-Produktion_lysis-purification_v1.jpg|center|700px|thumb|'''Fig. 1: Production of the S-Layer fusion proteins in E. coli.''' To build a cellfree Bisphenol A biosensor the S-Layer fusion proteins have to be extracted from the cells and purified (simplified schema).]]
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[[Image:Bielefeld_2011_S-Layer-Produktion_lysis-purification_v1.jpg|center|700px|thumb|'''Figure 1: Production of the S-layer fusion proteins in ''E. coli''.''' To build a cell-free bisphenol A biosensor the S-layer fusion proteins have to be extracted from the cells and purified (simplified schema).]]
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[[Image:Bielefeld_2011_Bead-Coating_v1.jpg|center|700px|thumb|'''Fig. 2: Coating of the silica beads with the S-Layer fusion proteins.''' Every silica bead gets covered by a geometric S-Layer film consisting of an alternating structure of the two essential S-Layer fusion proteins.]]
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[[Image:Bielefeld_2011_Bead-Coating_v1.jpg|center|700px|thumb|'''Figure 2: Coating of the silica beads with the S-layer fusion proteins.''' Every silica bead gets covered with a geometric S-layer film consisting of an alternating structure of the two essential S-layer fusion proteins.]]
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[[Image:IGEM_Bielefeld_Project.jpg|center|700px|thumb|'''Figure 3: Visualization of our cell-free bisphenol A biosensor system with all essential components.''' Bisphenol A (BPA) is reduced by the electrons from NADH transferred by the ferredoxin-NADP<sup>+</sup> oxidoreductase (FNR, <partinfo>BBa_K525499</partinfo>), ferredoxin (Fd, <partinfo>BBa_K123000</partinfo>) and cytochrome P450 (CYP, <partinfo>BBa_K123001</partinfo>) which are fused to a S-layer protein. The molecular beacon (hairpin structure) binds two short DNA oligos. The NAD<sup>+</sup>-dependent ligase (LigA, <partinfo>BBa_K525710</partinfo>), which is also fused to S-layer proteins, ligates the two oligos so that the hairpin structure opens up and the fluorophore is able to emit light after extinction.]]
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[[Image:IGEM_Bielefeld_Project.jpg|center|700px|thumb|'''Fig. 3: Visualization of our cellfree Bisphenol A biosensor system with all  essential components.''' Bisphenol A (BPA) is reduced by the electrons from NADH transfered by reductase (Red), ferredoxin (Fd) and cytochrome P450. The molecular beacon (hairpin structure) binds two short DNA-oligos. The NAD<sup>+</sup> dependent ligase (LigA) ligates the two oligos so that the hairpin structure opens up and the fluorophore is able to emit light.]]
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==Data for our favorite new parts==
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# <partinfo>K525305</partinfo> - '''Fusion protein of S-layer SgsE and mCitrine''': This fluorescent S-layer fusion protein is used to characterize purification methods and to demonstrate the S-layers ability to self-assemble on surfaces.
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# <partinfo>K525515</partinfo> - '''Fusion protein of BisdA and BisdB''': This fusion protein improves the bisphenol A degradation in ''E. coli'' compared to the so far in the partsregistry existing BPA degrading BioBricks.  
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# <partinfo>K525710</partinfo> - '''NAD<sup>+</sup>-dependent DNA ligase from ''E. coli'' (LigA) ''': This enzyme enables determination of NAD<sup>+</sup> even in very low concentrations by introducing it to a molecular beacon based bioassay.
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==Data For Our Favorite New Parts==
 
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# [http://partsregistry.org/Part:BBa_K525305 Main Page] - '''Fusion Protein of S-Layer SgsE and mCitrine''': This fluorescent S-layer fusion protein is used to characterize purification methods and to demonstrate the S-layer's ability to self-assemble on surfaces.
 
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# [http://partsregistry.org/Part:BBa_K525517 Main Page] - '''Fusion Protein of BisdA and BisdB (expressed)''': This fusion protein improves the bisphenol A degradation in ''E. coli'' compared to the so far in the partsregistry existing BPA degrading BioBricks.
 
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# [http://partsregistry.org/Part:BBa_K525710 Main Page] - '''NAD<sup>+</sup>-dependent DNA ligase from ''E. coli'' ''': This enzyme enables determination of NAD<sup>+</sup> even in very low concentrations by coupling it with a molecular beacon based assay.
 
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==Data for pre-existing parts==
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# [http://partsregistry.org/Part:BBa_K123000:Experience Experience] - '''BisdA degrades Bisphenol A when used with BisdB, BBa_K123000''' (University of Alberta, iGEM 2008): Complete degradation of 120 mg L<sup>-1</sup> Bisphenol A with polycistronic ''bisdAB'' gene in 30 - 33 h. Even faster (21 - 24 h) when using a fusion protein of BisdA and BisdB.
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# [http://partsregistry.org/Part:BBa_K123001:Experience Experience] - '''BisdB degrades Bisphenol A when used with BisdA, BBa_K123001''' (University of Alberta, iGEM 2008): Complete degradation of 120 mg L<sup>-1</sup> Bisphenol A with polycistronic ''bisdAB'' gene in 30 - 33 h. Even faster (21 - 24 h) when using a fusion protein of BisdA and BisdB.
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==Data For Pre-existing Parts==
 
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# [http://partsregistry.org/Part:BBa_K123000:Experience Experience] - '''BisdA degrades Bisphenol A when used with BisdB, BBa_K123000''' (University of Alberta, iGEM 2008): Complete degradation of 120 mg L<sup>-1</sup> Bisphenol A with polycistronic ''bisdAB'' gene in 30-33 h. Even faster (21-24 h) when using a fusion protein of BisdA and BisdB.
 
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# [http://partsregistry.org/Part:BBa_K123001:Experience Experience] - '''BisdB degrades Bisphenol A when used with BisdA, BBa_K123001''' (University of Alberta, iGEM 2008): Complete degradation of 120 mg L<sup>-1</sup> Bisphenol A with polycistronic ''bisdAB'' gene in 30-33 h. Even faster (21-24 h) when using a fusion protein of BisdA and BisdB.
 
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==We have also characterized the following parts==
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==We've Also Characterized the Following Parts==
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# <partinfo>K525405</partinfo> - '''Fusion protein of S-layer SbpA and mCitrine''': This fluorescent S-layer fusion protein is used to characterize purification methods and to demonstrate the S-layers ability to self-assemble on surfaces.
-
# [http://partsregistry.org/Part:BBa_K525405 Main Page] - '''Fusion Protein of S-Layer SbpA and mCitrine''': This fluorescent S-layer fusion protein is used to characterize purification methods and to demonstrate the S-layer's ability to self-assemble on surfaces.
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# <partinfo>K525512</partinfo> - '''Polycistronic expression of BisdA and BisdB''': This is the version of BPA degrading BioBricks found in the partsregistry - comparison to our fusion protein <partinfo>K525515</partinfo>.
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# [http://partsregistry.org/Part:BBa_K525512 Main Page] - '''Polycistronic expression of BisdA and BisdB''': This is the version of BPA degrading BioBricks found in the partsregistry - comparison to our fusion protein <partinfo>K525515</partinfo>.
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# <partinfo>K525517</partinfo> - '''Fusion Protein of BisdA and BisdB (expressed)''': This fusion protein improves the bisphenol A degradation in ''E. coli'' compared to the so far in the partsregistry existing BPA degrading BioBricks.
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# <partinfo>K525234</partinfo> - '''Fusion protein of S-layer CspB and mRFP''': This fluorescent S-layer fusion protein is used to characterize the intracellular localisation as well as purification methods for CspB S-layers from ''Corynebacterium halotolerans''.
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# <partinfo>K525121</partinfo> - '''S-layer protein CspB with TAT-sequence and lipid anchor''': This fluorescent S-layer fusion protein is used to characterize the intracellular localisation and purification methods for CspB S-layers from ''Corynebacterium glutamicum''.
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# <partinfo>K525123</partinfo> - '''S-layer protein CspB with lipid anchor''': This fluorescent S-layer fusion protein is used to characterize the intracellular localisation and purification methods for CspB S-layers from ''Corynebacterium glutamicum''.
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# <partinfo>K525222</partinfo> - '''S-layer protein CspB''': This fluorescent S-layer fusion protein is used to characterize the intracellular localisation and purification methods for CspB S-layers from ''Corynebacterium halotolerans''.
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# <partinfo>BBa_K525223</partinfo> - '''S-layer protein CspB with lipid anchor''': This fluorescent S-layer fusion protein is used to characterize the intracellular localisation and purification methods for CspB S-layers from ''Corynebacterium halotolerans''.
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# <partinfo>K525224</partinfo> - '''S-layer protein CspB with TAT-sequence''': This fluorescent S-layer fusion protein is used to characterize the intracellular localisation and purification methods for CspB S-layers from ''Corynebacterium halotolerans''.
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# <partinfo>K525304</partinfo> - '''Fusion protein of S-layer SbpA and mCherry''': Characterization of induction and expression profiles of this S-layer fusion protein.
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# <partinfo>K525306</partinfo> - '''Fusion protein of S-layer SgsE and mCerulean''': Characterization of induction and expression profiles of this S-layer fusion protein.
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# <partinfo>K525406</partinfo> - '''Fusion protein of S-layer SbpA and mCerulean''': Characterization of induction and expression profiles of this S-layer fusion protein.
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# <partinfo>K525311</partinfo> - '''Fusion protein of S-layer SgsE and firefly luciferase''': Characterization of induction and expression profiles, purification and stability of luciferase activity of this S-layer fusion protein.
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# <partinfo>K525551</partinfo> - '''Polycistronic expression of FNR, BisdA and BisdB''': Characterization of the BPA degradation ability of this device.
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# <partinfo>K525562</partinfo> - '''Expression of fusion protein of FNR, BisdA and BisdB''': Characterization of the BPA degradation ability of this device.
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# <partinfo>K525582</partinfo> - '''Polycistronic expression of FNR and fusion protein BisdA and BisdB''': Characterization of the BPA degradation ability of this device.

Latest revision as of 20:54, 28 October 2011

This page gives a basic overview about our cell-free bisphenol A biosensor system and the BioBricks we have used. A more detailed description of the biosensor system can be found in our project description as well as in the bisphenol A, S-layer and NAD+ detection background subsections.

Contents

How our system works

Figure 1: Production of the S-layer fusion proteins in E. coli. To build a cell-free bisphenol A biosensor the S-layer fusion proteins have to be extracted from the cells and purified (simplified schema).
Figure 2: Coating of the silica beads with the S-layer fusion proteins. Every silica bead gets covered with a geometric S-layer film consisting of an alternating structure of the two essential S-layer fusion proteins.
Figure 3: Visualization of our cell-free bisphenol A biosensor system with all essential components. Bisphenol A (BPA) is reduced by the electrons from NADH transferred by the ferredoxin-NADP+ oxidoreductase (FNR, <partinfo>BBa_K525499</partinfo>), ferredoxin (Fd, <partinfo>BBa_K123000</partinfo>) and cytochrome P450 (CYP, <partinfo>BBa_K123001</partinfo>) which are fused to a S-layer protein. The molecular beacon (hairpin structure) binds two short DNA oligos. The NAD+-dependent ligase (LigA, <partinfo>BBa_K525710</partinfo>), which is also fused to S-layer proteins, ligates the two oligos so that the hairpin structure opens up and the fluorophore is able to emit light after extinction.

Data for our favorite new parts

  1. <partinfo>K525305</partinfo> - Fusion protein of S-layer SgsE and mCitrine: This fluorescent S-layer fusion protein is used to characterize purification methods and to demonstrate the S-layers ability to self-assemble on surfaces.
  2. <partinfo>K525515</partinfo> - Fusion protein of BisdA and BisdB: This fusion protein improves the bisphenol A degradation in E. coli compared to the so far in the partsregistry existing BPA degrading BioBricks.
  3. <partinfo>K525710</partinfo> - NAD+-dependent DNA ligase from E. coli (LigA) : This enzyme enables determination of NAD+ even in very low concentrations by introducing it to a molecular beacon based bioassay.


Data for pre-existing parts

  1. [http://partsregistry.org/Part:BBa_K123000:Experience Experience] - BisdA degrades Bisphenol A when used with BisdB, BBa_K123000 (University of Alberta, iGEM 2008): Complete degradation of 120 mg L-1 Bisphenol A with polycistronic bisdAB gene in 30 - 33 h. Even faster (21 - 24 h) when using a fusion protein of BisdA and BisdB.
  2. [http://partsregistry.org/Part:BBa_K123001:Experience Experience] - BisdB degrades Bisphenol A when used with BisdA, BBa_K123001 (University of Alberta, iGEM 2008): Complete degradation of 120 mg L-1 Bisphenol A with polycistronic bisdAB gene in 30 - 33 h. Even faster (21 - 24 h) when using a fusion protein of BisdA and BisdB.


We have also characterized the following parts

  1. <partinfo>K525405</partinfo> - Fusion protein of S-layer SbpA and mCitrine: This fluorescent S-layer fusion protein is used to characterize purification methods and to demonstrate the S-layers ability to self-assemble on surfaces.
  2. <partinfo>K525512</partinfo> - Polycistronic expression of BisdA and BisdB: This is the version of BPA degrading BioBricks found in the partsregistry - comparison to our fusion protein <partinfo>K525515</partinfo>.
  3. <partinfo>K525517</partinfo> - Fusion Protein of BisdA and BisdB (expressed): This fusion protein improves the bisphenol A degradation in E. coli compared to the so far in the partsregistry existing BPA degrading BioBricks.
  4. <partinfo>K525234</partinfo> - Fusion protein of S-layer CspB and mRFP: This fluorescent S-layer fusion protein is used to characterize the intracellular localisation as well as purification methods for CspB S-layers from Corynebacterium halotolerans.
  5. <partinfo>K525121</partinfo> - S-layer protein CspB with TAT-sequence and lipid anchor: This fluorescent S-layer fusion protein is used to characterize the intracellular localisation and purification methods for CspB S-layers from Corynebacterium glutamicum.
  6. <partinfo>K525123</partinfo> - S-layer protein CspB with lipid anchor: This fluorescent S-layer fusion protein is used to characterize the intracellular localisation and purification methods for CspB S-layers from Corynebacterium glutamicum.
  7. <partinfo>K525222</partinfo> - S-layer protein CspB: This fluorescent S-layer fusion protein is used to characterize the intracellular localisation and purification methods for CspB S-layers from Corynebacterium halotolerans.
  8. <partinfo>BBa_K525223</partinfo> - S-layer protein CspB with lipid anchor: This fluorescent S-layer fusion protein is used to characterize the intracellular localisation and purification methods for CspB S-layers from Corynebacterium halotolerans.
  9. <partinfo>K525224</partinfo> - S-layer protein CspB with TAT-sequence: This fluorescent S-layer fusion protein is used to characterize the intracellular localisation and purification methods for CspB S-layers from Corynebacterium halotolerans.
  10. <partinfo>K525304</partinfo> - Fusion protein of S-layer SbpA and mCherry: Characterization of induction and expression profiles of this S-layer fusion protein.
  11. <partinfo>K525306</partinfo> - Fusion protein of S-layer SgsE and mCerulean: Characterization of induction and expression profiles of this S-layer fusion protein.
  12. <partinfo>K525406</partinfo> - Fusion protein of S-layer SbpA and mCerulean: Characterization of induction and expression profiles of this S-layer fusion protein.
  13. <partinfo>K525311</partinfo> - Fusion protein of S-layer SgsE and firefly luciferase: Characterization of induction and expression profiles, purification and stability of luciferase activity of this S-layer fusion protein.
  14. <partinfo>K525551</partinfo> - Polycistronic expression of FNR, BisdA and BisdB: Characterization of the BPA degradation ability of this device.
  15. <partinfo>K525562</partinfo> - Expression of fusion protein of FNR, BisdA and BisdB: Characterization of the BPA degradation ability of this device.
  16. <partinfo>K525582</partinfo> - Polycistronic expression of FNR and fusion protein BisdA and BisdB: Characterization of the BPA degradation ability of this device.
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