Difference between revisions of "Part:BBa K1031021"

 
(17 intermediate revisions by 2 users not shown)
Line 5: Line 5:
  
  
== Construction of our hybrid promoter ==
+
== '''Construction of our hybrid promoter''' ==
 
+
The hybrid promoter is constructed for the band-pass filter. A band-pass filter can be theoretically summarized as an incoherent feed forward loop, consisted of a positive loop and a negative loop. '''(Fig. 1)'''As for the reporter node, a special promoter is used so that the reporter can be controlled by the activator and inhibitor both. 
+
 
+
Band-pass filter constructed by Peking iGEM 2013 team: http://2013.igem.org/Team:Peking/Project/BandpassFilter
+
 
<html>
 
<html>
<img src="https://static.igem.org/mediawiki/igem.org/4/4b/Peking2013_model9.png", width=500px;/>
+
<p>
</html>
+
We modified a bacteriophage ϕR73’s <em>P<sub>2</sub></em> promoter into a hybrid promoter that can be activated by the ϕR73&delta; activator and repressed by the repressor cI simultaneously and put reporter sfGFP under its regulation. We constructed the hybrid promoter by replacing the sequence between position -1 and -25  of <em>P<sub>2</sub></em> promoter with the cI binding site <em>OR1</em> from Phage &lambda; <em>P<sub>R</sub></em> promoter. When ϕR73&delta; activator binds to its target sequence upstream of -35 element of the hybrid promoter, the transcription will start. The binding of cI dimers downstream of -35 element will block the binding of &sigma;<sup>70</sup> factors and thus repress the transcription even when ϕR73&delta; is bound. (<B>Fig. 1</B>). </p>
 
+
'''Fig.1''': The basic topology of band-pass filter, a positive loop and a negative loop is shown. The yellow arrow indicates activation and black line indicates inhibition. A and B nodes are determined by parameter sensitivity analysis. this part represents the reporter, shown in the bottom of the picture.
+
 
+
 
+
After deciding the circuit and protein to use, we started to design the promoter that could be activated by phiR73δ and be repressed by cI. To obtain a promoter, a hybrid promoter is required for the reporter node. We modified bacteriophage φR73’s promoter into a hybrid promoter that can be activated by the PhiR73 delta activator and repressed by the repressor cI respectively. We replaced the sequence between the -10 and -35 elements with the cI binding site Or1 from Phage λ. PhiR73δ activator binds to its binding site and the transcription starts. The binding of cI dimers will block the binding of σ70 factors and therefore repress the transcription (Fig.2).  
+
 
+
https://static.igem.org/mediawiki/2013/4/4f/Peking2013_Construction_of_hybrid_promoter.png
+
 
+
'''Figure 2'''.The construction of our hybrid promoter.
+
 
+
Based on this construction, when the input signal is weak, the concentration of PhiR73 delta is too low to generate a strong output. When the input signal is medium, despite a portion of promoters occupied by cI dimmers, the rest still can be activated by PhiR73 delta and bring about a visible output. When the input signal is strong, almost all of the promoters are “conquered” by cI dimers. The transcription is blocked and the output is shut down. Hence only medium input signal can generate a significant output and the Band Pass Filter was made.
+
  
 +
<img src="https://static.igem.org/mediawiki/2013/b/bf/Peking2013_hybrid_promoter_2.2.png" style="width:800px;margin-left:60px" ></a>
  
 +
<p style="text-align:center">
 +
<B>Figure.1</B> Construction of Our Hybrid Promoter.</br> Sequence information of phage &phi;R73 <em>P<sub>2</sub></em> promoter (<b>a</b>), phage &lambda; <em>P<sub>R</sub></em> promoter (<b>b</b>) and our hybrid promoter (<b>c</b>) are shown. <b>a</b>, In the <em>P<sub>2</sub></em> promoter, &phi;R73&delta; binds to a region between position -42 and -71 and activates transcription. <b>b</b>, In <em>P<sub>R</sub></em> promoter, cI dimer binds to <em>OR1</em> site (marked as blue) between position -9 and -25, blocking binding of  &sigma;<sup>70</sup> factors and inhibiting transcription. cI binding region indicates the sequence we used to replace the corresponding region in <em>P<sub>2</sub></em> promoter.<b>c</b>, The hybrid promoter is constructed by replacing sequence between position -1 and -25 of &phi;R73 <em>P<sub>2</sub></em> promoter with sequence at the same position in phage &lambda; <em>P<sub>R</sub></em> promoter that contains an <em>OR1</em> site. The hybrid promoter is co-regulated by &phi;R73&delta; and cI, with &phi;R73&delta; activating and cI repressing. The repression of cI dominates over the activation of  &phi;R73&delta;, since the steric hindrance created by cI dimer prevents formation of  transcription initiation complex even when RNA polymerases are recruited through the help of  &phi;R73&delta;.
 +
</p>
 +
</html>
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here
Line 40: Line 30:
 
<partinfo>BBa_K1031021 parameters</partinfo>
 
<partinfo>BBa_K1031021 parameters</partinfo>
 
<!-- -->
 
<!-- -->
 +
 +
=='''Characterization'''==
 +
<html>
 +
<p id ="Content9">
 +
To comprehensively characterize the dynamic performance of the hybrid promoter, we put two regulators of the hybrid promoter,  ϕR73&delta; and cI, under the control of two different inducible promoters, <em>P<sub>sal</sub></em> promoter and <em>P<sub>tac</sub></em> promoter. (<b>Fig.2</b>). This enables us to manipulate separately the expression levels of two regulatory proteins through tuning <em>P<sub>sal</sub></em> and <em>P<sub>tac</sub></em> promoter by adding different concentration combinations of inducers (salicylic acid for <em>P<sub>sal</sub></em> promoter and IPTG for <em>P<sub>tac</sub></em> promoter).
 +
</p>
 +
<img src="https://static.igem.org/mediawiki/2013/d/d2/Peking2013_bandpass_figure1_better.png" style="width:800px;margin-left:60px" ></a>
 +
<p style="text-align:center">
 +
<b>Figure.2</b> Testing construct for hybrid promoter.</br> &phi;R73&delta; was put under the regulation of <em>P<sub>sal</sub></em> promoter and cI was put under the control of <em>P<sub>tac</sub></em> promoter. Salicylic acid (SaA) will induce &phi;R73&delta; expression and activate the hybrid promoter. Isopropyl β-D-1-thiogalactopyranoside (IPTG) will induce cI expression and repress the hybrid promoter. Expression level of the two regulatory proteins can be manipulated separately by adding different concentration combinations of SaA and IPTG.
 +
</p>
 +
</br>
 +
<p id = "Content10">
 +
To comprehensively characterized the hybrid promoter's transcription activity,  we exposed the characterization circuit (<b>Fig.2</b>) to a 8x8 two-dimensional induction assay established by combining 8 different concentrations of salicylic acid and 8 different concentrations of IPTG and measured the fluorescence intensity of sfGFP reporter using Flow Cytometry. (<b>Fig.3</b>)
 +
</p>
 +
<img src="https://static.igem.org/mediawiki/2013/3/3f/Peking2013_bandpass_figure_2Dassay.png" style="width:800px;margin-left:60px" ></a>
 +
<p style="text-align:center">
 +
<b>Figure.3</b> Characterization of hybrid promoter's dynamic performance.</br> A two-dimensional inducer concentration assay was established by combining 8 different SaA concentrations (0, 0.1, 0.5, 1, 5, 10, 50 and 100&micro;M) with 8 different IPTG concentrations (0, 1, 10, 50, 100, 150, 200 and 300&micro;M). Bacteria cells expressing the testing construct were exposed to the assay and sfGFP fluorescence intensity was measured using Flow Cytometry. For a fixed IPTG concentration,  fluorescence intensity gradually increased as SaA concentration increased. For a fixed SaA concentration , fluorescence intensity gradually decreased as IPTG concentration increased. These features indicated that the promoter functioned as expected.
 +
</p>
 +
</br>
 +
<p id = "Content10">
 +
The hybrid promoter worked as expected. For a fixed IPTG concentration, the sfGFP fluorescence gradually increased as the salicylic acid concentration increased, exhibiting a Hill-function type dose-response curve. For a fixed high salicylic acid concentration under which sfGFP expression is visibly induced, the fluorescence gradually decreased as the IPTG concentration increased, also exhibiting a Hill-function type dose-response curve. These data prove that the hybrid promoter can indeed be activated by ϕR73&delta; and repressed by cI, and the repressing effect of cI protein dominates over the activating effect of  ϕR73&delta; protein, because transcription of the hybrid promoter can still be repressed to a very low level by cI even when  ϕR73&delta; is expressed at a very high level.
 +
</br>
 +
</br>
 +
We hypothesized that the negative feed-forward loop in the testing construct may actually represent a transformed version of the negative loop in the original Band-pass Filter construct. So we fit our model to the data from the testing construct in order to get real parameters for the Band-pass Filter circuit. (<b>Fig.4</b>)
 +
</p>
 +
<img src="https://static.igem.org/mediawiki/2013/8/82/Peking2013_bandpass_figure3_data_fitting.png" style="width:800px;margin-left:60px" ></a>
 +
<p style="text-align:center">
 +
<b>Figure.4</b> Model based data fitting for &phi;R73&delta; activator and cI repressor.</br> <b>a</b>, Experimental points are sfGFP fluorescence intensities under different SaA concentrations without IPTG. The model based fitting curve provided parameter values for n<sub>A'</sub> and K<sub>AG</sub>. <b>b</b>, Experimental points are sfGFP fluorescence intensities under different IPTG concentrations along with 100&micro;M SaA. Model based data fitting curve provided parameter values for n<sub>B'</sub>, K<sub>BG</sub> and k<sub>AG</sub>&bull;k<sub>BG</sub>. Fitting results: n<sub>A'</sub>=0.72705; K<sub>AG</sub>=62.99928; n<sub>B'</sub>=1.15498; K<sub>BG</sub>=11.53988; k<sub>AG</sub>&bull;k<sub>BG</sub>=24671.78415. Definitions for the parameters can be viewed in equations written in <a href="http://2013.igem.org/Team:Peking/Model">Model</a> page.
 +
</p>
 +
</br>
 +
<p id="Content 11">
 +
To test the activation effect of φR73δ, we constructed an activation circuit adopting <i>Psal</i>/NahR biosensor to regulate the expression of φR73δ. When exposed to inducers of NahR, <i>Psal</i> is initiated thus φR73δ is expressed. If φR73δ indeed activates the hybrid promoter, it is expected that the fluorescence intensity changes along with the change of inducers' concentration.   
 +
</p>
 +
<img src="https://static.igem.org/mediawiki/2013/thumb/4/47/Peking2013_part_Activation_loop.png/800px-Peking2013_part_Activation_loop.png"
 +
style="width:800px; margin-left:70px" />
 +
<p style="text-align:center"><b>Figure.5</b> Construction of activation circuit and corresponding data.</br> <b>Left</b>: Construction of activation circuit of Band-pass Filter. φR73δ is located on low-copy backbone pSB4K5 to avoid toxicity accumulation.</br> <b>Right</b>: Effect of activation circuit of Band-pass Filter. Horizontal axis stands for different concentrations of NahR inducer 4-MeSaA. Vertical axis represents induction ratio. It is obvious that φR74δ indeed activates the hybrid promoter, thus initiates the expression of sfGFP.
 +
</br>
 +
</br>
 +
<p id="Content 12">
 +
After confirming the activation effect of φR73δ, we then tested the inhibition effect of CⅠ protein to the hybrid promoter. A high basal level of fluorescence intensity was constructed via constitutive expression of φR73δ. Expression of CⅠ protein is regulated by inducer of NahR under <i>Psal</i> promoter. When exposed to inducers, the expression of CⅠ is supposed to inhibit the expression of reporter sfGFP if the hybrid promoter is indeed negatively regulated by CⅠ.
 +
</p>
 +
<img src="https://static.igem.org/mediawiki/2013/thumb/a/a5/Peking2013_part_Repression_loop.png/800px-Peking2013_part_Repression_loop.png"
 +
style="width:800px; margin-left:70px" />
 +
<p style="text-align:center"><b>Figure.6</b> Construction of inhibition circuit and corresponding data. </br> <b>Left</b>: Construction of inhibition circuit of Band-pass Filter, consisting of constitutive φR73δ, inducible CⅠ protein and reporter gene sfGFP under the control of hybrid promoter. </br> <b>Right</b>: Effect of inhibition circuit of Band-pass Filter. Horizontal axis stands for different concentrations of NahR inducer 4-MeSaA. Vertical axis represents induction ratio. It is obvious that CⅠ indeed inhibits the hybrid promoter, thus reduces the expression of sfGFP.
 +
</html>

Latest revision as of 20:00, 28 October 2013

Hybrid Promoter for Band-pass Filter

hybrid promoter for the band-pass filter


Construction of our hybrid promoter

We modified a bacteriophage ϕR73’s P2 promoter into a hybrid promoter that can be activated by the ϕR73δ activator and repressed by the repressor cI simultaneously and put reporter sfGFP under its regulation. We constructed the hybrid promoter by replacing the sequence between position -1 and -25 of P2 promoter with the cI binding site OR1 from Phage λ PR promoter. When ϕR73δ activator binds to its target sequence upstream of -35 element of the hybrid promoter, the transcription will start. The binding of cI dimers downstream of -35 element will block the binding of σ70 factors and thus repress the transcription even when ϕR73δ is bound. (Fig. 1).

Figure.1 Construction of Our Hybrid Promoter.
Sequence information of phage φR73 P2 promoter (a), phage λ PR promoter (b) and our hybrid promoter (c) are shown. a, In the P2 promoter, φR73δ binds to a region between position -42 and -71 and activates transcription. b, In PR promoter, cI dimer binds to OR1 site (marked as blue) between position -9 and -25, blocking binding of σ70 factors and inhibiting transcription. cI binding region indicates the sequence we used to replace the corresponding region in P2 promoter.c, The hybrid promoter is constructed by replacing sequence between position -1 and -25 of φR73 P2 promoter with sequence at the same position in phage λ PR promoter that contains an OR1 site. The hybrid promoter is co-regulated by φR73δ and cI, with φR73δ activating and cI repressing. The repression of cI dominates over the activation of φR73δ, since the steric hindrance created by cI dimer prevents formation of transcription initiation complex even when RNA polymerases are recruited through the help of φR73δ.

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 AgeI site found at 16
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 127


Characterization

To comprehensively characterize the dynamic performance of the hybrid promoter, we put two regulators of the hybrid promoter, ϕR73δ and cI, under the control of two different inducible promoters, Psal promoter and Ptac promoter. (Fig.2). This enables us to manipulate separately the expression levels of two regulatory proteins through tuning Psal and Ptac promoter by adding different concentration combinations of inducers (salicylic acid for Psal promoter and IPTG for Ptac promoter).

Figure.2 Testing construct for hybrid promoter.
φR73δ was put under the regulation of Psal promoter and cI was put under the control of Ptac promoter. Salicylic acid (SaA) will induce φR73δ expression and activate the hybrid promoter. Isopropyl β-D-1-thiogalactopyranoside (IPTG) will induce cI expression and repress the hybrid promoter. Expression level of the two regulatory proteins can be manipulated separately by adding different concentration combinations of SaA and IPTG.


To comprehensively characterized the hybrid promoter's transcription activity, we exposed the characterization circuit (Fig.2) to a 8x8 two-dimensional induction assay established by combining 8 different concentrations of salicylic acid and 8 different concentrations of IPTG and measured the fluorescence intensity of sfGFP reporter using Flow Cytometry. (Fig.3)

Figure.3 Characterization of hybrid promoter's dynamic performance.
A two-dimensional inducer concentration assay was established by combining 8 different SaA concentrations (0, 0.1, 0.5, 1, 5, 10, 50 and 100µM) with 8 different IPTG concentrations (0, 1, 10, 50, 100, 150, 200 and 300µM). Bacteria cells expressing the testing construct were exposed to the assay and sfGFP fluorescence intensity was measured using Flow Cytometry. For a fixed IPTG concentration, fluorescence intensity gradually increased as SaA concentration increased. For a fixed SaA concentration , fluorescence intensity gradually decreased as IPTG concentration increased. These features indicated that the promoter functioned as expected.


The hybrid promoter worked as expected. For a fixed IPTG concentration, the sfGFP fluorescence gradually increased as the salicylic acid concentration increased, exhibiting a Hill-function type dose-response curve. For a fixed high salicylic acid concentration under which sfGFP expression is visibly induced, the fluorescence gradually decreased as the IPTG concentration increased, also exhibiting a Hill-function type dose-response curve. These data prove that the hybrid promoter can indeed be activated by ϕR73δ and repressed by cI, and the repressing effect of cI protein dominates over the activating effect of ϕR73δ protein, because transcription of the hybrid promoter can still be repressed to a very low level by cI even when ϕR73δ is expressed at a very high level.

We hypothesized that the negative feed-forward loop in the testing construct may actually represent a transformed version of the negative loop in the original Band-pass Filter construct. So we fit our model to the data from the testing construct in order to get real parameters for the Band-pass Filter circuit. (Fig.4)

Figure.4 Model based data fitting for φR73δ activator and cI repressor.
a, Experimental points are sfGFP fluorescence intensities under different SaA concentrations without IPTG. The model based fitting curve provided parameter values for nA' and KAG. b, Experimental points are sfGFP fluorescence intensities under different IPTG concentrations along with 100µM SaA. Model based data fitting curve provided parameter values for nB', KBG and kAG•kBG. Fitting results: nA'=0.72705; KAG=62.99928; nB'=1.15498; KBG=11.53988; kAG•kBG=24671.78415. Definitions for the parameters can be viewed in equations written in Model page.


To test the activation effect of φR73δ, we constructed an activation circuit adopting Psal/NahR biosensor to regulate the expression of φR73δ. When exposed to inducers of NahR, Psal is initiated thus φR73δ is expressed. If φR73δ indeed activates the hybrid promoter, it is expected that the fluorescence intensity changes along with the change of inducers' concentration.

Figure.5 Construction of activation circuit and corresponding data.
Left: Construction of activation circuit of Band-pass Filter. φR73δ is located on low-copy backbone pSB4K5 to avoid toxicity accumulation.
Right: Effect of activation circuit of Band-pass Filter. Horizontal axis stands for different concentrations of NahR inducer 4-MeSaA. Vertical axis represents induction ratio. It is obvious that φR74δ indeed activates the hybrid promoter, thus initiates the expression of sfGFP.

After confirming the activation effect of φR73δ, we then tested the inhibition effect of CⅠ protein to the hybrid promoter. A high basal level of fluorescence intensity was constructed via constitutive expression of φR73δ. Expression of CⅠ protein is regulated by inducer of NahR under Psal promoter. When exposed to inducers, the expression of CⅠ is supposed to inhibit the expression of reporter sfGFP if the hybrid promoter is indeed negatively regulated by CⅠ.

Figure.6 Construction of inhibition circuit and corresponding data.
Left: Construction of inhibition circuit of Band-pass Filter, consisting of constitutive φR73δ, inducible CⅠ protein and reporter gene sfGFP under the control of hybrid promoter.
Right: Effect of inhibition circuit of Band-pass Filter. Horizontal axis stands for different concentrations of NahR inducer 4-MeSaA. Vertical axis represents induction ratio. It is obvious that CⅠ indeed inhibits the hybrid promoter, thus reduces the expression of sfGFP.