Difference between revisions of "Part:BBa K1617000"

 
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<partinfo>BBa_K1617000 short</partinfo>
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<b>Flagellin</b> is the filament forming component of bacterial flagellas. The up to 20 µm long filaments are formed by the self-assembly of flagellin. Flagellin proteins consist of four domains (D0-D3). While the D0 and D1 domains are well conserved, the D2 and D3 domains are highly variable in sequence and length. Here, we created an modular flagellin with an easily replacable D3 region. A multi-cloning side flanking the D3 domain allows the design of costume-made flagellins by being compatible to iGEM fusion standards such as RFC25 and RFC21.
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<br><br><b> You can pick any RFC25 compatible BioBrick from the registry and test its functionality immidiatally via an easy motility assay.</b>
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<br><br>
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One flagella usually carries about  flavone from grapefruits. In plants, it is synthesized from tyrosine and is one of the central metabolites in the flavone biosynthesis. It is able to reduce the oxidative stress and inhibit some P450 enzymes. One of these cytochrome P450 enzymes is involved in the degradation of caffeine and increases the effect of caffeine after the inhibition with naringenin. 
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<br><br>
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<b>FdeR</b> is a homo dimeric protein from <i>Herbaspirillum seropedicae</i>. In the presence of naringenin (or naringenin chalcone), FdeR activates the specific promoter region upstream of the FdeR region and induces a strong gene expression. <br> In  <i>Herbaspirillum seropedicae</i> the FdeR activates the Fde-Operon (Fde: Flavanone degradation) and enables the growth with naringenin and the naringenin chalcone. 
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<br><br>
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When GFP or another reporter protein is cloned downstream of this part, it can be used as an <i>in vivo</i> naringenin sensor.
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src="https://static.igem.org/mediawiki/2008/0/0f/Ecoli_filament.jpg"></p>
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      <br>
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      <p class="MsoCaption" align="text-align:justify"><span lang="EN-US"><b>Figure 1</b></span></a><span lang="EN-US">
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Flow chart of the FdeR activated GFP expression. The constitutively expressed the FdeR monomers form homodimers. Naringenin molecules bind to the FdeR homodimer and induce a conformational change of the homodimeric FdeR structure. This conformational change activates FdeR, which is now able to bind to the uncharacterized promoter region.  Binding to the promoter region induces expression of genes downstream of the fdeR promoter region. </span></p>
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===Usage and Biology===
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You can use the reporters for measuring naringenin concentrations in your samples.
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Depending on which fluorophor you want to detect, you can use one of three biosensors:
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<br><br><br>
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<ul class="aufz10">
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  <li class="block-10vi">A: with CFP response use         <a href="/Part:BBa_K1497022">BBa_K1497022</a></li>
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  <li class="block-10vi">B: with mKate response use <a href="/Part:BBa_K1497021">BBa_K1497021</a></li>
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  <li class="block-10vi">C: with no reporter              <a href="/Part:BBa_K1497019">BBa_K1497019</a></li>
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  <li class="block-10vi">D: with GFP response use          <a href="/Part:BBa_K1497020">BBa_K1497020</a></li>
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src="https://static.igem.org/mediawiki/2014/8/89/Petridischnaringenin.png"></p>
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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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<i>E. coli</i> 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 fluorophor. Right: On agar plate with 100 µM naringenin under UV light. The fluorescence of GFP, CFP and mKate is visible. <br></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.
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===Functional Parameters===
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The Biobrick <html><a href="/Part:BBa_K1497019">BBa_K1497019</a></html> produces in <i>E. coli</i> B and K strains the FdeR Protein. The iGEM Team TU Darmstadt 2014 measured the fluorescense of GFP and mKate after the incubation with diffrent conentrations of naringenin. The results are shown in Figure 3. 
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src="https://static.igem.org/mediawiki/2014/3/32/Narinmrfpgfp.png"></p>
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      <br>
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      <p class="MsoCaption" align="text-align:justify"><span lang="EN-US"><b>Figure 3</b></span></a><span lang="EN-US">
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<b>Left:</b> Characterization of  <a href="/Part:BBa_K1497020">BBa_K1497020</a>. GFP fluorescence depends on the concentration of naringenin. We measured the GFP fluorescence after 16 h incubation with different concentrations of naringenin. By setting higher concentrations of naringenin, we gained higher fluorescence of GFP as well. <b>Right:</b> Characterization of <a href="/Part:BBa_K1497021">BBa_K1497021</a>. mKate (<a href="/Part:BBa_K1055000">BBa_K1055000</a>) fluorescence depends on the concentration of naringenin. We measured the mKate (<a href="/Part:BBa_K1055000">BBa_K1055000</a>) fluorescence after 16 h incubation with different concentrations of naringenin. By setting higher concentrations of naringenin, we gained higher fluorescence of mKate as well.</span></p>
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====In vivo characterisation of the naringenin biosynthesis operon (<html><a href="/Part:BBa_K1497007">BBa_K1497007</a></html>)====
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iGEM TU Darmstadt 2014 reconstitute the naringenin biosynthesis in <i>E. coli</i> by construction of a operon polycistronic gene cluster (<a href="/Part:BBa_K1497007">BBa_K1497007</a>) under control of the strong T7 promoter (<a href="/Part:BBa_K1497017">BBa_K1497017</a>). They used the naringenin biosensor with GFP response <a href="/Part:BBa_K1497020">K1497020</a> to characterize the naringenin biosynthesis operon in <i>E. coli</i> BL21(DE3). <br><br> The result are shown in figure 4. The GFP fluorescene is only in the cells with the T7 naringenin operon visible and detectable. The team determined for this operon a naringenin production yield of 3 µmol naringenin per liter.   
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      <img src="https://static.igem.org/mediawiki/2014/1/12/Naringenint7balken.png" align="right"
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      <br><br>
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      <p class="MsoCaption" align="text-align:justify"><span lang="EN-US"><b>Figure 4</b></span></a><span lang="EN-US">
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<b>Left: </b>Cell pellets with and without T7-Naringenin operon from <i>E. coli</i> BL21(DE3)-pSB1C3-<i>fdeR-gfp</i>. By using ultraviolet light the pellet containing the naringenin operon shows a GFP fluorescence. <b>Right: </b>Measurement of the GFP fluorescence in the<i>E. coli</i> BL21(DE3)-pSB1C3-<i>fdeR-gfp</i> strain containing and not containing the T7-Naringenin operon.
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= Contructing a multimodular Flagellin =
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[[File:]]
  
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== 1 Theory ==
 
  
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=== 1.1 Aim ===
 
  
 
Design of a functional flaggelin variant which does not contain  the variable d3 flagellin domain anymore but instead carries a polylinker region (MCS). This polylinker region is the product of an inserted multi cloning side in place of the endogeneous d3 coding sequence.
 
Design of a functional flaggelin variant which does not contain  the variable d3 flagellin domain anymore but instead carries a polylinker region (MCS). This polylinker region is the product of an inserted multi cloning side in place of the endogeneous d3 coding sequence.

Revision as of 06:07, 18 September 2015

Modular Flagellin - FliC_MCS

Flagellin is the filament forming component of bacterial flagellas. The up to 20 µm long filaments are formed by the self-assembly of flagellin. Flagellin proteins consist of four domains (D0-D3). While the D0 and D1 domains are well conserved, the D2 and D3 domains are highly variable in sequence and length. Here, we created an modular flagellin with an easily replacable D3 region. A multi-cloning side flanking the D3 domain allows the design of costume-made flagellins by being compatible to iGEM fusion standards such as RFC25 and RFC21.

You can pick any RFC25 compatible BioBrick from the registry and test its functionality immidiatally via an easy motility assay.

One flagella usually carries about flavone from grapefruits. In plants, it is synthesized from tyrosine and is one of the central metabolites in the flavone biosynthesis. It is able to reduce the oxidative stress and inhibit some P450 enzymes. One of these cytochrome P450 enzymes is involved in the degradation of caffeine and increases the effect of caffeine after the inhibition with naringenin.

FdeR is a homo dimeric protein from Herbaspirillum seropedicae. In the presence of naringenin (or naringenin chalcone), FdeR activates the specific promoter region upstream of the FdeR region and induces a strong gene expression.
In Herbaspirillum seropedicae the FdeR activates the Fde-Operon (Fde: Flavanone degradation) and enables the growth with naringenin and the naringenin chalcone.

When GFP or another reporter protein is cloned downstream of this part, it can be used as an in vivo naringenin sensor.


Figure 1 Flow chart of the FdeR activated GFP expression. The constitutively expressed the FdeR monomers form homodimers. Naringenin molecules bind to the FdeR homodimer and induce a conformational change of the homodimeric FdeR structure. This conformational change activates FdeR, which is now able to bind to the uncharacterized promoter region. Binding to the promoter region induces expression of genes downstream of the fdeR promoter region.



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:




Figure 2 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 fluorophor. Right: On agar plate with 100 µM naringenin under UV light. The fluorescence of GFP, CFP and mKate is visible.

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

The Biobrick BBa_K1497019 produces in E. coli B and K strains the FdeR Protein. The iGEM Team TU Darmstadt 2014 measured the fluorescense of GFP and mKate after the incubation with diffrent conentrations of naringenin. The results are shown in Figure 3.


Figure 3 Left: Characterization of BBa_K1497020. GFP fluorescence depends on the concentration of naringenin. We measured the GFP fluorescence after 16 h incubation with different concentrations of naringenin. By setting higher concentrations of naringenin, we gained higher fluorescence of GFP as well. Right: Characterization of BBa_K1497021. mKate (BBa_K1055000) fluorescence depends on the concentration of naringenin. We measured the mKate (BBa_K1055000) fluorescence after 16 h incubation with different concentrations of naringenin. By setting higher concentrations of naringenin, we gained higher fluorescence of mKate as well.



In vivo characterisation of the naringenin biosynthesis operon (BBa_K1497007)


iGEM TU Darmstadt 2014 reconstitute the naringenin biosynthesis in E. coli by construction of a operon polycistronic gene cluster (BBa_K1497007) under control of the strong T7 promoter (BBa_K1497017). They used the naringenin biosensor with GFP response K1497020 to characterize the naringenin biosynthesis operon in E. coli BL21(DE3).

The result are shown in figure 4. The GFP fluorescene is only in the cells with the T7 naringenin operon visible and detectable. The team determined for this operon a naringenin production yield of 3 µmol naringenin per liter.



Figure 4 Left: Cell pellets with and without T7-Naringenin operon from E. coli BL21(DE3)-pSB1C3-fdeR-gfp. By using ultraviolet light the pellet containing the naringenin operon shows a GFP fluorescence. Right: Measurement of the GFP fluorescence in theE. coli BL21(DE3)-pSB1C3-fdeR-gfp strain containing and not containing the T7-Naringenin operon.


[[File:]]


Design of a functional flaggelin variant which does not contain the variable d3 flagellin domain anymore but instead carries a polylinker region (MCS). This polylinker region is the product of an inserted multi cloning side in place of the endogeneous d3 coding sequence.



Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 628
    Illegal BamHI site found at 577
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 583
    Illegal AgeI site found at 634
  • 1000
    COMPATIBLE WITH RFC[1000]