Difference between revisions of "Part:BBa K1497019"
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FdeR is a homo dimeric protein from ''Herbaspirillum seropedicae''. In present of naringenin, FdeR activates the specific promotor region upstream of the fdeR region and allow a strong gene expression.  
 
FdeR is a homo dimeric protein from ''Herbaspirillum seropedicae''. In present of naringenin, FdeR activates the specific promotor region upstream of the fdeR region and allow a strong gene expression.  
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      <p class="MsoCaption" align="text-align:justify"><span lang="EN-US"><b>Figure 2</b></span></a><span lang="EN-US">
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Flow chart of the FdeR activated gfp expression. The constitutive expression of fdeR forms the homodimeric FdeR protein. In present of naringenin, , naringenin molecules bind to the FdeR protein and operate a conformational change of the homodimeric FdeR structure. This conformational change activates FdeR, which is now enabled to bind to the uncharacterized promotor domain.  Binding to the promotor domain induces expression of genes, which are cloned behind fdeR promtor region. </span></p>
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   [[File:Homology_model_of_FdeR.png|300px|thumb|right|Homology model of FdeR. PDB: 2ESN was used as template. ]]
 
   [[File:Homology_model_of_FdeR.png|300px|thumb|right|Homology model of FdeR. PDB: 2ESN was used as template. ]]
 
Based on this reporter protein and 3 different fluorescence proteins, we designed 3 new biosensors for in vivo detection and determination of naringenin.  
 
Based on this reporter protein and 3 different fluorescence proteins, we designed 3 new biosensors for in vivo detection and determination of naringenin.  
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       <p class="MsoCaption" align="text-align:justify"><span lang="EN-US"><b>Figure 2</b></span></a><span lang="EN-US">
 
       <p class="MsoCaption" align="text-align:justify"><span lang="EN-US"><b>Figure 2</b></span></a><span lang="EN-US">
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Flow chart of the FdeR activated gfp expression. The constitutive expression of fdeR forms the homodimeric FdeR protein. In present of naringenin, , naringenin molecules bind to the FdeR protein and operate a conformational change of the homodimeric FdeR structure. This conformational change activates FdeR, which is now enabled to bind to the uncharacterized promotor domain. Binding to the promotor domain induces expression of genes, which are cloned behind fdeR promtor region. </span></p>
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X E. coli Top10 with different Naringenin biosensors. Left: On agar plate without naringenin no colour is visible. Middle: On agar plate with 100 µM naringenin colour is visible, except of negative sample <a href="/Part:BBa_K1497019">BBa_K1497019</a> without fluorphor. Right: On agar plate with 100 µM Naringenin under UV light. The fluorescence of GFP, CFP and mKate is visible. <br>(A: <a href="/Part:BBa_K1497022">BBa_K1497022</a> B: <a href="/Part:BBa_K1497021">BBa_K1497021</a> C: <a href="/Part:BBa_K1497019">BBa_K1497019</a> D: <a href="/Part:BBa_K1497020">BBa_K1497020</a>). </span></p>
 
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You can create your own naringenin sensor or your own naringenin dependent gene expression device as well. For these reasons use the Biobrick <html><a href="/Part:BBa_K1497019">K1497019</a></html> and clone your parts of interest (without RBS!) behind the device.
 
You can create your own naringenin sensor or your own naringenin dependent gene expression device as well. For these reasons use the Biobrick <html><a href="/Part:BBa_K1497019">K1497019</a></html> and clone your parts of interest (without RBS!) behind the device.

Revision as of 22:49, 9 October 2014

fdeR (Naringenin binding protein) and fde operon regulatory domain

FdeR is a homo dimeric protein from Herbaspirillum seropedicae. In present of naringenin, FdeR activates the specific promotor region upstream of the fdeR region and allow a strong gene expression.



Figure 2 Flow chart of the FdeR activated gfp expression. The constitutive expression of fdeR forms the homodimeric FdeR protein. In present of naringenin, , naringenin molecules bind to the FdeR protein and operate a conformational change of the homodimeric FdeR structure. This conformational change activates FdeR, which is now enabled to bind to the uncharacterized promotor domain. Binding to the promotor domain induces expression of genes, which are cloned behind fdeR promtor region.


Homology model of FdeR. PDB: 2ESN was used as template.

Based on this reporter protein and 3 different fluorescence proteins, we designed 3 new biosensors for in vivo detection and determination of naringenin.



Usage and Biology

You can use the reporters for measuring naringenin concentrations in your samples. Depending on which fluorophor you want to detect, you can use one of three biosensors:


  • with GFP response use BBa_K1497020
  • with mKate response use BBa_K1497021
  • with CFP response use BBa_K1497022



    • Figure 2 X E. coli Top10 with different Naringenin biosensors. Left: On agar plate without naringenin no colour is visible. Middle: On agar plate with 100 µM naringenin colour is visible, except of negative sample BBa_K1497019 without fluorphor. Right: On agar plate with 100 µM Naringenin under UV light. The fluorescence of GFP, CFP and mKate is visible.
    (A: BBa_K1497022 B: BBa_K1497021 C: BBa_K1497019 D: BBa_K1497020).

    You can create your own naringenin sensor or your own naringenin dependent gene expression device as well. For these reasons use the Biobrick K1497019 and clone your parts of interest (without RBS!) behind the device.


    Functional Parameters

    Sequence and Features


    Assembly Compatibility:
    • 10
      COMPATIBLE WITH RFC[10]
    • 12
      COMPATIBLE WITH RFC[12]
    • 21
      COMPATIBLE WITH RFC[21]
    • 23
      COMPATIBLE WITH RFC[23]
    • 25
      INCOMPATIBLE WITH RFC[25]
      Illegal NgoMIV site found at 95
      Illegal NgoMIV site found at 452
      Illegal NgoMIV site found at 543
      Illegal NgoMIV site found at 555
    • 1000
      INCOMPATIBLE WITH RFC[1000]
      Illegal BsaI.rc site found at 271