Difference between revisions of "Part:BBa K1847011"
 
(10 intermediate revisions by the same user not shown)
Line 19: Line 19:
  
 
<h1>Usage and Biology</h1>
 
<h1>Usage and Biology</h1>
−
[[File:ETH15_Double_promoter_scheme.png|thumb|right|400px|Scheme of the activity of the double promoter.]]
+
[[File:ETH15_Double_promoter_scheme.png|thumb|right|300px|Figure 1. Scheme of the activity of the double promoter.]]
 
<p>The natural promoter of LldR ([[Part:BBa_K822000]]) consists of two operators (O1 and O2) and a promoter which is intercalated between the operators. It regulates the expression of the <i>lldPRD</i> operon, and it is involved in L-lactate metabolism. This promoter is repressed by a dimer of LldR, possibly by forming a DNA loop that does not allow the RNA polymerase to bind to the promoter. LldR can also have a function as an activator [1]. The repression of the promoter can be removed by lactate.</p>  
 
<p>The natural promoter of LldR ([[Part:BBa_K822000]]) consists of two operators (O1 and O2) and a promoter which is intercalated between the operators. It regulates the expression of the <i>lldPRD</i> operon, and it is involved in L-lactate metabolism. This promoter is repressed by a dimer of LldR, possibly by forming a DNA loop that does not allow the RNA polymerase to bind to the promoter. LldR can also have a function as an activator [1]. The repression of the promoter can be removed by lactate.</p>  
−
The lac operator is repressed by LacI. This repression can be removed by allolactose or by IPTG.  
+
Our biobrick is a hybrid promoter repressed by LldR and LacI.
  
 
<h1>Characterization of the promoter</h1>
 
<h1>Characterization of the promoter</h1>
−
We wanted to know how the promoter would respond to the lactate presence and to IPTG, and how important is the architecture of the promoter in this response. For this regard, we built several promoters. [[Part:BBa_K1847010]], [[Part:BBa_K1847011]], and [[Part:BBa_K1847012]].  
+
We wanted to know how the promoter would respond to the presence of lactate and/or IPTG, and how important is the architecture of the promoter in this response. For this regard, we built several promoters. [[Part:BBa_K1847010]], [[Part:BBa_K1847011]], and [[Part:BBa_K1847012]].  
  
−
<h2>Experimental Set-Up</h2>
+
<h2>Experimental results</h2>
 +
This promoter is only responsive to lactate, as can be seen in the figure below. Therefore, it is not useful as a double sensor.
 +
[[File:ETH15_PromoterAND.png|thumb|left|500px|Figure 2. Expected result for the hybrid promoter]]
 +
[[File:ETH15_CombinedPromoterUV5.png|thumb|400px|center|Figure 3. Fluorescence output under different concentrations of lactate and IPTG.]]
 +
 
 +
<h2>Experimental Set-Up for LldR response</h2>
 
<h3>Plasmids</h3>
 
<h3>Plasmids</h3>
−
<p>To test our double promoter we designed a plasmid containing the promoter with sfGFP in a medium copy plasmid pSEVA261 and transformed it into <i>Escherichia coli</i> TOP10. Then, we added a second plasmid containing lldR with a medium strong promoter (BBa_J23118) and a strong RBS (BBa_B0034) in pSEVA371 backbone. Finally, we transformed another plasmid with LacI. We expect LldR and LacI to repress the promoter. Upon addition of IPTG, LacI repression will be removed. Upon addition of lactate, LldR repression will be removed. Only when the two inducers are present GFP can get expressed. </p>
+
<p>To test our double promoter we designed a plasmid containing the promoter with sfGFP in a medium copy plasmid and transformed it into <i>Escherichia coli</i> TOP10. Then, we added a second plasmid containing lldR and LldP with a medium strong promoter ([[Part:BBa_J23118]]) and a strong RBS ([[Part:BBa_B0034]]). Finally, we transformed another plasmid with LacI. LldR and LacI will repress the promoter. Upon addition of IPTG, LacI repression will be removed. Upon addition of lactate, LldR repression will be removed. Only when the two inducers are present GFP can get expressed. </p>
−
<p>We tried another set-up in which we added LldP into our LldR plasmid. LldP is an L-lactate permease which import L-lactate into the cell.
+
−
In summary, we tried our system in three different conditions:</p>
+
−
<ul>
+
−
  <li>Plasmid with the double promoter and sfGFP in pSEVA261 + J23118-B0034-lldR in pSEVA371</li>
+
−
  <li>Plasmid with the double promoter and sfGFP in pSEVA261 + J23114-B0032-lldP-lldR (LldP and LldR are under the control of the same promoter) in pSEVA371</li>
+
−
  <li>Plasmid with the double promoter and sfGFP in pSEVA261 + J23118-B0032-lldP-lldR (LldP and LldR are under the control of the same promoter) in pSEVA371</li>
+
−
  <li>Plasmid with the double promoter and sfGFP in pSEVA261 + J23118-B0032-lldP-lldR (LldP and LldR are under the control of the same promoter) in pSEVA371 + lacI</li>
+
−
</ul>
+
  
 
<h3>Plate reader</h3>
 
<h3>Plate reader</h3>
−
<i>E. coli</i> TOP10 strains were grown overnight in Lysogeny Broth (LB) containing kanamycin (1 &micro;/mL), chloramphenicol (0.36 &micro;/mL) and ampicillin (1 &micro;/mL) as required at 37&deg;C and 200 rpm. Cultures were diluted 1:50 in fresh LB with the corresponding antibiotic and transferred to a 96-well plate (200 &micro;L/well). Cultures were grown for 90 min to arrive to exponential phase and then different concentrations of lactate were added. Samples were always made in triplicates and a blank of LB with the corresponding lactate concentration was done. During 7 h the absorbance at OD600 and fluorescence (excitation 488 nm and emission 530 nm) were measured with intervals of 7 min. The plate was always kept at 37&deg;C. We calculated dose-response curves from the exponential phase of the bacteria.
+
<i>E. coli</i> TOP10 strains were grown overnight in Lysogeny Broth (LB) containing kanamycin (50 &micro;g/mL), chloramphenicol (12.5 &micro;g/mL) and ampicillin (50 &micro;g/mL) as required at 37&deg;C and 200 rpm. Cultures were diluted 1:50 in fresh LB with the corresponding antibiotic and transferred to a 96-well plate (200 &micro;L/well). Cultures were grown for 90 min to arrive to exponential phase and then different concentrations of lactate were added. A blank of LB with the corresponding lactate concentration was done. During 7 h the absorbance at OD600 and fluorescence (excitation 488 nm and emission 530 nm) were measured with intervals of 7 min. The plate was always kept at 37&deg;C in a Tecan Infinite M200 Pro Plate Reader. We calculated dose-response curves from the exponential phase of the bacteria using normalized fluorescence by optical density.  
−
 
+
−
<h2>Modeling</h2>
+
−
Each experimental data set was fitted to a Hill function using the Least Absolute Residual method (Fitting Toolbox in MatLab).
+
−
[[File:ETH15_equation.png|center|300px]]
+
−
 
+
−
Where:
+
−
<ul>
+
−
    <li>al: leakiness in &micro;M/min</li>
+
−
    <li>mu: constant in &micro;M/min</li>
+
−
    <li>Km: half-maximum effective concentration (a representation of sensitivity) in &micro;M</li>
+
−
    <li>n: Hill coefficient (a representation of cooperativity), unitless</li>
+
−
</ul>
+
−
 
+
−
{|class="wikitable"
+
−
|-
+
−
! !!J23118-B0034-lldR!!J23118-B0034-lldP-lldR!!J23114-B0032-lldP-lldR
+
−
|-
+
−
! rowspan="4" scope="row" | Coefficient values
+
−
| K=491.7  (91.34, 892) || K=2442  (511.1, 4373) || K=457.7  (271.7, 643.8)
+
−
|-
+
−
| al =  2220  (931.5, 3509)||al = 2396  (769.3, 4023)||al = 1.32e+04  (fixed at bound)
+
−
|-
+
−
| mu =  8758  (7552, 9964)||mu = 1.57e+04  (9270, 2.212e+04)||mu = 6942  (5920, 7963)
+
−
|-
+
−
| n1 =    0.7  (fixed at bound)|| n1 =  1.156  (0.4928, 1.82)||n1 = 1.569  (-0.05875, 3.196)
+
−
|-
+
−
!rowspan="5" scope="row"|Goodness to fit
+
−
|  sse:5.0244e+08||sse: 1.2664e+09||sse: 1.2386e+09
+
−
|-
+
−
|rsquare: 0.9767||rsquare: 0.9852||rsquare: 0.9569
+
−
|-
+
−
|dfe: 8||dfe: 7|| dfe: 8
+
−
|-
+
−
|adjrsquare: 0.9708||adjrsquare: 0.9788||adjrsquare: 0.9461
+
−
|-
+
−
|rmse: 7.9250e+03||rmse: 1.3450e+04||rmse: 1.2443e+04
+
−
|}
+
−
 
+
−
<div style="margin:auto;width:880px">
+
−
<ul>
+
−
<li class="graphthumb" style="display:inline-block;width:33%">[[Image:ETH15_P74_LldR.png|thumb|260px|Dose-response curve for our promoter with J23118-B0034-lldR]]</li>
+
−
<li class="graphthumb" style="display:inline-block;width:33%">[[Image:P74_LldPRlow.png|thumb|260px|Dose-response curve for our promoter with J23114-B0032-lldP-lldR]]</li>
+
−
<li class="graphthumb" style="display:inline-block;width:33%">[[Image:ETH15_P74_LldPRhi.png|thumb|260px|Dose-response curve for our promoter with J23118-B0032-lldP-lldR]]</li>
+
−
</ul>
+
−
 
+
−
As you can see from the graphs, activation with only LldR is lower than with LldP-LldR. Also, the sample with LldP-LldR with a stronger promoter achieves higher fluorescence levels. We believe that this is due to the fact that more molecules of LldP are produced and therefore more lactate can enter inside the cell. Just as a qualitative example, J23118-B0034-lldR has half of the maximum fluorescence than J23118-B0034-lldP-lldR.
+
−
When comparing J23114-B0034-lldP-lldR and J23118-B0034-lldP-lldR, we can see that J23114-B0034-lldP-lldR has more leakiness, which we think is due to its low expression, and therefore it cannot repress the gene properly.  
+
  
 
<h1>References</h1>
 
<h1>References</h1>

Latest revision as of 22:32, 27 September 2015

lldRO1-placUV5-lacO-lldRO2

Promoter regulated by LldR and LacI.

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
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]



Usage and Biology

Figure 1. Scheme of the activity of the double promoter.

The natural promoter of LldR (Part:BBa_K822000) consists of two operators (O1 and O2) and a promoter which is intercalated between the operators. It regulates the expression of the lldPRD operon, and it is involved in L-lactate metabolism. This promoter is repressed by a dimer of LldR, possibly by forming a DNA loop that does not allow the RNA polymerase to bind to the promoter. LldR can also have a function as an activator [1]. The repression of the promoter can be removed by lactate.

Our biobrick is a hybrid promoter repressed by LldR and LacI.

Characterization of the promoter

We wanted to know how the promoter would respond to the presence of lactate and/or IPTG, and how important is the architecture of the promoter in this response. For this regard, we built several promoters. Part:BBa_K1847010, Part:BBa_K1847011, and Part:BBa_K1847012.

Experimental results

This promoter is only responsive to lactate, as can be seen in the figure below. Therefore, it is not useful as a double sensor.

Figure 2. Expected result for the hybrid promoter
Figure 3. Fluorescence output under different concentrations of lactate and IPTG.

Experimental Set-Up for LldR response

Plasmids

To test our double promoter we designed a plasmid containing the promoter with sfGFP in a medium copy plasmid and transformed it into Escherichia coli TOP10. Then, we added a second plasmid containing lldR and LldP with a medium strong promoter (Part:BBa_J23118) and a strong RBS (Part:BBa_B0034). Finally, we transformed another plasmid with LacI. LldR and LacI will repress the promoter. Upon addition of IPTG, LacI repression will be removed. Upon addition of lactate, LldR repression will be removed. Only when the two inducers are present GFP can get expressed.

Plate reader

E. coli TOP10 strains were grown overnight in Lysogeny Broth (LB) containing kanamycin (50 µg/mL), chloramphenicol (12.5 µg/mL) and ampicillin (50 µg/mL) as required at 37°C and 200 rpm. Cultures were diluted 1:50 in fresh LB with the corresponding antibiotic and transferred to a 96-well plate (200 µL/well). Cultures were grown for 90 min to arrive to exponential phase and then different concentrations of lactate were added. A blank of LB with the corresponding lactate concentration was done. During 7 h the absorbance at OD600 and fluorescence (excitation 488 nm and emission 530 nm) were measured with intervals of 7 min. The plate was always kept at 37°C in a Tecan Infinite M200 Pro Plate Reader. We calculated dose-response curves from the exponential phase of the bacteria using normalized fluorescence by optical density.

References

  1. J Bacteriol. 2008 Apr; 190(8): 2997–3005.

</div>