Difference between revisions of "Part:BBa K1031911"

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<partinfo>BBa_K1031911 short</partinfo>
 
<partinfo>BBa_K1031911 short</partinfo>
  
'''Overview'''
 
  
XylS is an archetype transcriptional activator of AraC/XylS family, mined from the TOL plasmid pWW0 of the bacterium Pseudomonas putida. It is composed of a C-terminal domain (CTD) involved in DNA binding containing two helix-turn-helix motifs and an N-terminal domain required for effector binding and protein dimerization.
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== '''Introduction''' ==
XylS detects benzoate and its’ derivatives, mainly methyl and chlorine substitutes at 2-, 3- carbon.
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XylS is an archetype transcriptional activator of AraC/XylS family, mined from the TOL plasmid pWW0 of the bacterium <i>Pseudomonas putida</i>. It is composed of a C-terminal domain (CTD) involved in DNA binding, and an N-terminal domain required for effector binding and protein dimerization<html><a href="#ReferenceXylS"><sup>[1]</sup></a></html>. XylS detect benzoate and its’ derivatives, mainly methyl and chlorine substitution at 2-, 3- carbon<html><a href="#ReferenceXylS"><sup>[2]</sup></a></html>.
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<img src="https://static.igem.org/mediawiki/igem.org/8/85/Peking2013_Xyls_figure1.png", width=600px; />
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<img src="https://static.igem.org/mediawiki/igem.org/8/85/Peking2013_Xyls_figure1.png" style="width:600px;margin-left:160px"  ></a>
<p></p>
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<p style="text-align:center"><b>Figure.1</b> Regulatory circuits controlled by XylS and XylR on the TOL plasmid pWW0<a href="#ReferenceXylS"><sup>[3]</sup></a>.  
'''Fig. 1''' Regulatory circuits controlling the expression from the TOL plasmid pWW0[7].  
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Squares, XylS; circles, XylR; open symbol,s.transcriptional regulator without aromatic effector binding; closed symbols, effector-bound transcription factors that is in active form. See the main text for the detailed explanation for the regulatory loops<a href="#ReferenceXylS"><sup>[4]</sup></a>.
Squares, XylS; circles, XylR; open symbol,s.transcriptional regulator without aromatics effector binding; closed symbols, effector-bound transcription factors that is in active form. See the main text for the detailed explanation for regulatory loops.
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</p></html>.
  
 
'''Promoter Structure'''
 
'''Promoter Structure'''
  
The cognate promoter regulated by XylS, Pm, is σ70-dependent in E.coli, while in Pseudomonas putida, it is σ32/38-dependent[6]. It acts as the master regulator to control the ON/OFF expression of meta-operon on TOL plasmid pWW0[2]. In this meta-operon, XylXYZLTEGFJQKIH genes encode enzymes for the degradation of benzoate and its derivatives, generating intermediate products in TCA cycle. (Fig 1)
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The cognate promoter regulated by XylS, <i>Pm</i>, is σ<sup>54</sup>- dependent in <i>Pseudomonas putida</i>; meanwhile in <i>E.coli</i>, it is σ<sup>70</sup>- dependent<html><a href="#ReferenceXylS"><sup>[5]</sup></a></html>. It acts as the master regulator to control the ON/OFF expression of meta-operon on TOL plasmid pWW0<html><a href="#ReferenceXylS"><sup>[3]</sup></a></html>. In this meta-operon, XylXYZLTEGFJQKIH genes encode enzymes for the degradation of benzoate and its derivatives, producing intermediate metabolites as carbon sources (<b>Fig.1</b>).
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'''Mechanism'''
 
'''Mechanism'''
  
 
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<html>
<img id="XylSFigure3" src="https://static.igem.org/mediawiki/igem.org/a/a3/Peking2013_Xyls_figure3.png", width=600px; />
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<img src="https://static.igem.org/mediawiki/igem.org/a/a3/Peking2013_Xyls_figure3.png" style="width:600px;margin-left:160px"  ></a>
<p></p>
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<p style="text-align:center"><b>Figure.2</b> Mechanism of XylS binding to Pm promoter.<br/>
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Mechanism of transcription activation by XylS at <i>Pm</i> promoter. <b>Step 1</b>: Free DNA. The -10/-35 consensus boxes of σ<sup>70</sup>-dependent promoter and the two XylS binding sites (D: distal; and P: proximal) are highlighted. The bending angle is supposed to be 35°, centered at XylS proximal binding site. <b>Step 2</b>: A first XylS monomer binds to <i>Pm</i> at the proximal site, shifts the bent center to the DNA sequence between the two XylS binding sites, and increases the bending angle to 50°. <b>Step 3</b>: This conformational change facilitates the binding of a second XylS monomer to the distal site, further increasing the DNA curvature to an overall value of 98°. <b>Step 4</b>: Contacts with RNAP, also probably with the σ-subunit, are established through the α-CTD of RNA polymerase, which dramatically facilitates the open complex formation and transcription initiation.
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</p>
 
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</html>
'''Fig 2.'''  Mechanism of XylS binding to Pm promoter
 
  
Mechanism transcription activation by XylS at Pm promoter. Step 1: Free DNA. The -10/-35 consensus sequence motifs of σ70-dependent promoter and the two XylS binding sites (D: distal; and P: proximal) are depicted. The bending angle is supposed to be 35°, centered at the XylS proximal binding site. Step 2: A first XylS monomer binds to Pm at the proximal site, shifts the bent center to the DNA sequence between the two XylS binding sites, and increases the bending angle to 50°. Step 3: This change favors the binding of a second monomer to the distal site, further increasing the DNA curvature to an overall value of 98° (here schematized as a right angle). Contacts with RNAP, also probably with the σ-subunit, are established through the α-CTD, which dramatically facilitates the open complex formation and transcription initiation as shown in Step 4.
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== '''Tuning of Biosensor''' ==
 
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'''Tuning of Biosensor'''
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<img id="XylSFigure4" src="https://static.igem.org/mediawiki/igem.org/6/68/Peking2013_Xyls_figure4.png", width=600px; />
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<img src="https://static.igem.org/mediawiki/2013/5/54/Peking2013_XylS_Constructure.png" style="width:800px;margin-left:60px"  ></a>
<p></p>
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<br/>
 
</html>
 
</html>
'''Fig 3 a.''' Construction of biosensor circuit. b.Induction ratio of XylS biosensor library that utilizes different constitutive Pc promoters to control the expression of XylS. Horizontal axis stands for different XylS biosensor with Pc promoters of different strength. The expression strength of these constitutive promoters, J23113, J23109, J23114, J23105, J23106 is 21, 106, 256, 623, and 1185, respectively, according to the Partsregistry. Four kinds of aromatics, namely BzO, 2-MxeBzO, 3-MeBzO and 4-MeBzO, shown with different color intensities, were tested following Test Protocol 1 (a hyper link is needed here). Vertical axis represents the ON-OFF induction ratio. The Pm/XylS biosensor circuit which adopted Pc promoter J23114 clearly
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<img src="https://static.igem.org/mediawiki/2013/9/93/Peking2013_XylS_Library.png" style="width:450px;margin-left:60px" ></a>
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<br/>
  
105-XylS-TT: https://parts.igem.org/Part:BBa_K1031912
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<p style="position: relative; top: -340px;left: 530px;width:330px">
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<b>Figure.3</b>(a) Construction of biosensor circuit.</br> (b) Using a library of constitutive promoters (<i>Pc</i>) to fine-tune the induction ratio of XylS biosensor. Horizontal axis stands for different XylS biosensor circuits with different <i>Pc</i> promoters. These <i>Pc</i> promoters are of different strength to control the expression of XylS. The relative expression strength of these constitutive promoters, J23113, J23109, J23114, J23105, J23106 are 21, 106, 256, 623, and 1185, respectively, according to the <a href="https://parts.igem.org/Part:BBa_J23119">Partsregistry</a>. Four kinds of aromatic compounds, namely BzO, 2-MxeBzO, 3-MeBzO and 4-MeBzO, shown with different color intensities, were tested following <a href="http://2013.igem.org/Team:Peking/Team/Notebook/Protocols#Content1">Test Protocol 1</a>. Vertical axis represents the ON-OFF induction ratio. The <i>Pm</i>/XylS biosensor circuit adopting a weak <i>Pc</i> promoter J23114 performed best throughout the four inducers.
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<p style="position: relative; top:-250px;left: 60px;">
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Related Part:</br>
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105-XylS-Terminator: <a href="https://parts.igem.org/Part:BBa_K1031912">https://parts.igem.org/Part:BBa_K1031912</a></br>
  
109-XylS-TT: https://parts.igem.org/Part:BBa_K1031913
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109-XylS-Terminator: <a href="https://parts.igem.org/Part:BBa_K1031913">https://parts.igem.org/Part:BBa_K1031913</a></br>
 
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114-XylS-TT: https://parts.igem.org/Part:BBa_K1031916
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114-XylS-Terminator: <a href="https://parts.igem.org/Part:BBa_K1031916">https://parts.igem.org/Part:BBa_K1031916</a></br>
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</p>
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<partinfo>BBa_K1031911 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K1031911 SequenceAndFeatures</partinfo>
  
'''Summary: ON/OFF test to 78 aromatic compounds'''
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== '''Characterization of Biosensor''' ==
  
20 compounds showed apparent activation effect with the induction ratios over 20, they are listed as follows: BzO, 2-MeBzO, 3-MeBzO, 4-MeBzO, 2-FBzO, 4-FBzO, 2-ClBzO, 3-ClBzO, 4-ClBzO, 2-BrBzO, 4-BrBzO, 3-IBzO, 3-MeOBzO, SaA, 3-MeOSaA, 4-ClSaA, 5-ClSaA, 3-MeBAD, 3-ClTOL '''(Fig 4)'''
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'''ON/OFF test to 78 aromatic compounds'''
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20 compounds showed apparent activation effect with the induction ratios over 20, they are listed as follows: BzO, 2-MeBzO, 3-MeBzO, 4-MeBzO, 2-FBzO, 4-FBzO, 2-ClBzO, 3-ClBzO, 4-ClBzO, 2-BrBzO, 4-BrBzO, 3-IBzO, 3-MeOBzO, SaA, 3-MeOSaA, 4-ClSaA, 5-ClSaA, 3-MeBAD, 3-ClTOL '''(Fig.4)'''
  
 
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<img id="XylSFigure5_1" src="https://static.igem.org/mediawiki/igem.org/f/f4/Peking2013_Xyls_figure5.1.png", width=500px; />
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<img src="https://static.igem.org/mediawiki/2013/f/f3/Peking2013_XylS_data.png" style="width:800px;margin-left:60px"  ></a>
<p></p>
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<br/>
<img id="XylSFigure5_2" style="position: relative; top:-320px; left: 560px; " style="position:relative; top: -300px; left: 520px; " src="https://static.igem.org/mediawiki/igem.org/a/a4/Peking2013_Xyls_figure5.2.PNG", width=350px; />
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<p style="text-align:center">
<p style="position: relative; top:-320px; "><b>Fig 5.</b> The detective range of Pm/J23114-XylS biosensor circuit. 
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<b>Figure.4</b> (a) The induction ratios of all 78 typical aromatic compounds in the <a href="http://2013.igem.org/Team:Peking/Team/Notebook/Protocols#Content3">ON/OFF test</a> following <a href="http://2013.igem.org/Team:Peking/Team/Notebook/Protocols#Content1">Test Protocol 1</a>. XylS biosensor could respond to 24 out of 78 aromatics with the induction ratio higher than 20, mainly benzoate, salicylic and their derivatives. </br>(b) The aromatics-sensing profile of XylS biosensor is summarized from (a), highlighted in red in the aromatics spectrum. The structure formula of typical inducers are listed around the central spectrum, near their chemical formula.  
</br>
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(a) The induction ratio column in the On-Off test following protocol 1. XylS could respond to 24 out of 78 aromatics with the induction ratio over 20, mainly benzoate, salicylic and their derivatives. (b) The detection range of sensor strain XylS is profiled in red at the aromatics spectrum. The structure formula of typical inducer is listed around the cycle spectrum, near its chemical formula.  
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</p>
 
</p>
 
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</br></br>
<p style="position: relative; top:-300px;" >
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<p>
 
<b>Dose-response curve to benzoate, salicylic acid and derivatives</b>
 
<b>Dose-response curve to benzoate, salicylic acid and derivatives</b>
 
</br>
 
</br>
Pm/J23114-XylS biosensor circuit was subjected to induction experiments with concentration of inducer ranging at 10 µM, 30µM,100µM, 300µM and 1000µM according to protocol 1. ''' (Fig 5).'''
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<i>Pm</i>/J23114-XylS biosensor circuit was subjected to induction experiments with concentration of inducer ranging at 10 µM, 30µM,100µM, 300µM and 1000µM according to <a href="http://2013.igem.org/Team:Peking/Team/Notebook/Protocols#Content1">Test Protocol 1</a>. (<b>Fig.5</b>).
 
</br>
 
</br>
<img src="https://static.igem.org/mediawiki/igem.org/9/93/Peking2013_Xyls_figure6.png", style="width:500px;"/>
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<img src="https://static.igem.org/mediawiki/2013/f/fd/Peking2013_XylS_Induce.png" style="width:800px;margin-left:60px" ></a>
 
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<br/>
<img id="XylSCurve2" src="https://static.igem.org/mediawiki/igem.org/6/67/Peking2013_Xyls_figur7.png" style="position:relative; top: -340px; left: 420px; ", width=500px; />
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</p>
<p style="position: relative; top: -600px;" >
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<p style="text-align:center">
<b>Fig. 5</b>  a.Dose-response curve of Pm/J23114-XylS biosensor circuit in response to benzoate and its derivatives. X-axis stands for concentration gradient of inducers at 10µM, 30µM, 100µM, 300µM and 1000µM. Different colors represent different kinds of inducers. Y-axis shows induction ratio reflected via fluorescence intensity.  
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<b>Figure.5</b>  (a) Dose-response curves of XylS biosensor induced by benzoate and its derivatives. X-axis stands for concentration gradient of inducers at 10µM, 30µM, 100µM, 300µM and 1000µM. Different colors represent different kinds of inducers. Y-axis shows induction ratios. (b) Dose-response curves of XylS biosensor induced by salicylate and its derivatives. X-axis stands for concentration gradient of inducers at 10µM, 30µM, 100µM, 300µM and 1000µM. Y-axis denotes induction ratios. Different colors denote different kinds of inducers.  
</br>
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b.Dose-response curve of Pm/J23114-XylS expression system in response to salicylate and its derivatives. X-axis stands for concentration gradient of inducers at 10µM, 30µM, 100µM, 300µM and 1000µM. Different colors represent different kinds of inducers. Y-axis shows induction ratio reflected via fluorescence intensity.  
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== Orthogonality ==
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== '''Orthogonality of Different Sensor''' ==
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If the presence of an inducer of biosensor A (not an inducer of biosensor B) doesn’t interfere with the dose response of biosensor B to any of its inducers, and vice versa, we call the B and A biosensors are "orthogonal"; namely, no synergistic/antagonistic effects happen between the inducers of A and B biosensors.(for more details, <a href="http://2013.igem.org/Team:Peking/Project/BioSensors/MulticomponentAnalysis">Chick Here</a>)
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<img src="https://static.igem.org/mediawiki/igem.org/2/24/Peking2013_MAFigure4.jpg"/>
  
<table border="1">
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<table border="1", style="position:relative; top: -200px; left: 400px;" >
 
<tr>
 
<tr>
 
<th>Sensor</th><th>Host</th><th>Main Inducers</th>
 
<th>Sensor</th><th>Host</th><th>Main Inducers</th>
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<td>HbpR</td><td><i>Pseudomonas azelaica</i></td><td>o-Phenylphenol 2,6'-DiHydroxybiphenol</td>
 
<td>HbpR</td><td><i>Pseudomonas azelaica</i></td><td>o-Phenylphenol 2,6'-DiHydroxybiphenol</td>
 
</tr>
 
</tr>
 
 
</table>
 
</table>
https://static.igem.org/mediawiki/igem.org/2/24/Peking2013_MAFigure4.jpg
 
  
we have confirmed the orthogonality among inducers of different biosensors, which is one of the main features we expect for our aromatics-sensing toolkit. Our sensors are well suited to multicomponent analysis.
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<p style="text-align:center; position: relative; top: -100px;">
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<B>Figure.6</B> Summary of the orthogonality assay to evaluate the synergistic/antagonistic effects between the inducers of 4 representative biosensors.</br> No synergistic or antagonistic effects between the inducers of 4 representative biosensors (XylS, NahR, HbpR, and DmpR) were observed. For instance, although the sensing profiles of NahR and XylS overlap to some extent, the NahR-specific and XylS-specific inducers proved to be really orthogonal.
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</p>
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<p style="position: relative; top: -80px;">
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We have confirmed the orthogonality among inducers of different biosensors, which is one of the main features we expect for our aromatics-sensing toolkit; this allowed the combination of these biosensors to profile aromatics for the ease of practical applications.
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'''Related Parts:'''
 
'''Related Parts:'''
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DmpR: http://2013.igem.org/Team:Peking/Project/BioSensors/DmpR
 
DmpR: http://2013.igem.org/Team:Peking/Project/BioSensors/DmpR
 
  
Orthoganaility between inducer A (originally detected by biosensor I) and B (originally detected by biosensor II) were tested in the following manner (Fig. 1). To test the effect of inducer B upon the dose-response curve of inducer A obtained by biosensor I:
 
  
(1) Fluorescence intensity of biosensor I elicited by inducer A of concentration gradient was measured as standard results''' (Fig. 1a, Lane 1)''';  
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We examined the orthogonality between 4 representative biosensors (<b>Fig.7</b>). The orthogonality test between two biosensors, biosensor I and biosensor II, was performed in the following procedure:
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</br></br>
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1. A typical inducer A for biosensor I and a typical inducer B for biosensor II were selected.<br/>
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2. The dose response of biosensor I to inducer A was measured, under the perturbation of inducer B.<br/>
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3. The dose-response of biosensor II to inducer B was measured, under the perturbation of inducer A.
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</br></br>
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If biosensor I and biosensor II are orthogonal, the dose response of biosensor I to inducer A should be constant, regardless of the concentrations of inducer B; and the dose response of biosensor II to inducer B should be constant, regardless of the concentrations of inducer A. Namely, for two "orthogonal" biosensors, the perturbation of an unrelated inducer has negligible effect on the dose response of a biosensor to its related inducer (<b>Fig.8</b>).
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<img src="https://static.igem.org/mediawiki/igem.org/4/45/Peking2013_MAFigure1.jpg" style="width:700px;margin-left:110px"  ></a>
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(2) And fluorescence intensity of biosensor I induced by inducer A of concentration gradient in the presence of a certain concentration of inducer B was measured (Fig. 1a, Lane 2 and 3) and compared with the standard results.  
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<b>Figure.7</b> Orthogonality test assay for inducer A (detected by biosensor I) and inducer B (detected by biosensor II). (a) Biosensor I was added into the test assay. Different mixtures of inducers were added into lane 1, 2, and 3 respectively as listed above. Effect of inducer B upon the dose-response curve of inducer A was tested by comparing the fluorescence intensity of biosensor I among lane 1 ,2, and 3. (b) Biosensor II was added into the test assay. Different mixtures of inducers were added into lane 1, 2, and 3 respectively as listed above. Effect of inducer A upon the dose-response curve of inducer B was tested by comparing the fluorescence intensity of biosensor II among lane 1 ,2, and 3.
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The effect of inducer A upon the dose-response curve of inducer B obtained by biosensor II was tested vice versa '''(Fig. 1b)'''.
 
  
https://static.igem.org/mediawiki/igem.org/4/45/Peking2013_MAFigure1.jpg
 
  
'''Fig. 1.''' Orthogonality test assay for inducer A (detected by biosensor I) and inducer B (detected by biosensor II). (a) Biosensor I was added into the test assay. Different mixtures of inducers were added into lane 1, 2, and 3 respectively as listed above. Effect of inducer B upon the dose-response curve of inducer A was tested by comparing the fluorescence intensity of biosensor I among lane 1 ,2, and 3. (b) Biosensor II was added into the test assay. Different mixtures of inducers were added into lane 1, 2, and 3 respectively as listed above. Effect of inducer A upon the dose-response curve of inducer B was tested by comparing the fluorescence intensity of biosensor II among lane 1 ,2, and 3.
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<img src="https://static.igem.org/mediawiki/igem.org/c/c7/Peking2013_Figure3ab.jpg" style="width:800px;margin-left:60px"  ></a>
  
We managed to demonstrate the orthogonality among inducers of different biosensors in a more quantitative and visible way. If inducer A and B were orthogonal, the fluorescence intensity should be identical no matter with or without the irrelevant inducer B. That is to say, the ideal experimental points should be aligned in a line whose slope is one.
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<p style="text-align:center">
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<B>Figure.8 </B>Correlation of the inducer B and the dose-response of biosensor I  to its inducer A. Each point on the right plot represents a concentration of inducer A. It's x coordinate represents the fluorescence when inducer B is 0 and the y coordinate represents the fluorescence when the cell is exposed to a none-zero concentration of inducer B. If the dose-response of biosensor I is invariant to the concentration of inducer B, the x coordinate of a experimental point should be equal to its y coordinate and the experimental points are supposed to be aligned in a line whose slope is one.
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The orithogonality of inducers of XylS, NahR, HbpR and DmpR biosensors have been carefully confirmed using the test assay introduced above '''(Fig. 2)'''. The experimental points were processed by linear fitting and the slopes of the fitting curves were compared with 1. The closer the slope was to 1, the more orthogonal the inducers were. The results showed that inducers of biosensor XylS and NahR '''(Fig. 3a, b)''', XylS and HbpR''' (Fig. 2c, d)''', NahR and HbpR '''(Fig. 2e, f)''', XylS and DmpR '''(Fig. 2g, h)''', NahR and DmpR '''(Fig. 2i, j)''', and HbpR and DmpR '''(Fig. 2k, l)''' are all highly orthogonal, which is summarized in '''Fig. 3.'''
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The orthogonality between XylS, NahR, HbpR and DmpR biosensors have been carefully evaluated using the assay discussed above (<b>Fig.7</b>). The data were processed by linear fitting and the slopes of the fitting curves were compared with 1 (<b>Fig.7, Fig.8</b>). The closer the slope was to 1, the more orthogonal the two biosensors were. Results showed that the biosensor pairs, XylS and NahR (<b>Fig.9a, b</b>), XylS and HbpR (<b>Fig.9c, d</b>), NahR and HbpR (<b>Fig.9e, f</b>), XylS and DmpR (<b>Fig.9g, h</b>), NahR and DmpR (<b>Fig.9i, j</b>), and HbpR and DmpR (<b>Fig.9k, l</b>) are all orthogonal, as summarized in <b>Fig.6</b>.
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https://static.igem.org/mediawiki/igem.org/c/c7/Peking2013_Figure3ab.jpg
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<img src="https://static.igem.org/mediawiki/igem.org/4/44/Peking2013_MAFigureef.jpg" style="width:800px;margin-left:60px"  ></a>
  
https://static.igem.org/mediawiki/igem.org/9/96/Peking2013_MAFigure3cd.jpg
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<img id="FigurePic6" src=" https://static.igem.org/mediawiki/2013/f/fb/Peking2013_Orthogonality_Fig._4%28g-h%29.png" style="width:800px;margin-left:60px"/>
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<img id="FigurePic7" src=" https://static.igem.org/mediawiki/2013/4/46/Peking2013_Orthogonality_Fig._4%28i-j%29.png" style="width:800px;margin-left:60px"/>
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<img id="FigurePic8" src=" https://static.igem.org/mediawiki/2013/1/15/Peking2013_Orthogonality_Fig._4%28k-l%29.png" style="width:800px;margin-left:60px"/>
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https://static.igem.org/mediawiki/igem.org/4/44/Peking2013_MAFigureef.jpg
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<B>Figure.9</B> Linear fitting of the data obtained from the orthogonality assay showing that the orthogonality between the 4 representative biosensors. The experiments and data processing were performed as described in <b>Fig. 7</b> and <b>Fig. 8</b>.The black dashed line denotes slope=1 as the reference line. These fittings showed the orthogonality between biosensors, (<b>a, b</b>) XylS and NahR; (<b>c, d</b>) XylS and HbpR; (<b>e, f</b>) NahR and HbpR, (<b>g, h</b>) XylS and DmpR, (<b>i, j</b>) NahR and DmpR, and (<b>k, l</b>) HbpR and DmpR. The experiment data, linear fitting curves of biosensor, and cognate inducers are in different colors: XylS in red, NahR in green, HbpR in orange and DmpR in dark cyan.
'''Fig. 3.''' Experimental points and the linear fitting curves of the orthogonality test. The black dashed lines are with the slopes of 1, showing as the reference line. The slopes of the experimental fitting curves were showed in the upside portion of the figure, all of them were around 1. These data showed the orthogonality among inducers of biosensors(a, b) XylS and NahR; (c, d) XylS and HbpR; (e, f) NahR and HbpR, (g, h) XylS and DmpR, (i, j) NahR and DmpR, and (k, l) HbpR and DmpR. The experimental points and linear fitting curves of biosensor and its inducers are marked in different colors: XylS in red, NahR in green, HbpR in orange and DmpR in dark cyan.
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== Reference ==
 
== Reference ==
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<html>
 
<p id="ReferenceXylS">
 
<p id="ReferenceXylS">
[1] Domínguez-Cuevas, P., Ramos, J. L., & Marqués, S. (2010). Sequential XylS-CTD binding to the Pm promoter induces DNA bending prior to activation. Journal of bacteriology, 192(11), 2682-2690. <br/>
+
[1] Kaldalu, N., Toots, U., de Lorenzo, V., & Ustav, M. (2000). Functional domains of the TOL plasmid transcription factor XylS. Journal of bacteriology, 182(4), 1118-1126.<br/>
[2] Kaldalu, N., Mandel, T., & Ustav, M. (1996). TOL plasmid transcription factor XylS binds specifically to the Pm operator sequence. Molecular microbiology,20(3), 569-579.<br/>
+
 
[3] Domínguez-Cuevas, P., Marín, P., Busby, S., Ramos, J. L., & Marqués, S. (2008). Roles of effectors in XylS-dependent transcription activation: intramolecular domain derepression and DNA binding. Journal of bacteriology, 190(9), 3118-3128.<br/>
+
[2] Ramos, J. L., Michan, C., Rojo, F., Dwyer, D., & Timmis, K. (1990). Signal-regulator interactions, genetic analysis of the effector binding site of xyls, the benzoate-activated positive regulator of Pseudomonas TOL plasmid meta-cleavage pathway operon. Journal of molecular biology, 211(2), 373-382.<br/>
[4] Ramos, J. L., Michan, C., Rojo, F., Dwyer, D., & Timmis, K. (1990). Signal-regulator interactions, genetic analysis of the effector binding site of xyls, the benzoate-activated positive regulator of Pseudomonas TOL plasmid meta-cleavage pathway operon. Journal of molecular biology, 211(2), 373-382.<br/>
+
 
[5] Kaldalu, N., Toots, U., de Lorenzo, V., & Ustav, M. (2000). Functional domains of the TOL plasmid transcription factor XylS. Journal of bacteriology, 182(4), 1118-1126.<br/>
+
[3] Ramos, J. L., Marqués, S., & Timmis, K. N. (1997). Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annual Reviews in Microbiology, 51(1), 341-373.<br/>
[6] Gerischer, U. (2002). Specific and global regulation of genes associated with the degradation of aromatic compounds in bacteria. Journal of molecular microbiology and biotechnology, 4(2), 111-122.<br/>
+
 
[7] Ramos, J. L., Marqués, S., & Timmis, K. N. (1997). Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annual Reviews in Microbiology, 51(1), 341-373.<br/>
+
[4] Domínguez-Cuevas, P., Marín, P., Busby, S., Ramos, J. L., & Marqués, S. (2008). Roles of effectors in XylS-dependent transcription activation: intramolecular domain derepression and DNA binding. Journal of bacteriology, 190(9), 3118-3128.<br/>
 +
 
 +
[5] Kaldalu, N., Mandel, T., & Ustav, M. (1996). TOL plasmid transcription factor XylS binds specifically to the Pm operator sequence. Molecular microbiology,20(3), 569-579.<br/>
 +
 
  
 
</p>
 
</p>

Latest revision as of 04:10, 28 September 2013

XylS-Terminator


Introduction

XylS is an archetype transcriptional activator of AraC/XylS family, mined from the TOL plasmid pWW0 of the bacterium Pseudomonas putida. It is composed of a C-terminal domain (CTD) involved in DNA binding, and an N-terminal domain required for effector binding and protein dimerization[1]. XylS detect benzoate and its’ derivatives, mainly methyl and chlorine substitution at 2-, 3- carbon[2].

Figure.1 Regulatory circuits controlled by XylS and XylR on the TOL plasmid pWW0[3]. Squares, XylS; circles, XylR; open symbol,s.transcriptional regulator without aromatic effector binding; closed symbols, effector-bound transcription factors that is in active form. See the main text for the detailed explanation for the regulatory loops[4].

.

Promoter Structure

The cognate promoter regulated by XylS, Pm, is σ54- dependent in Pseudomonas putida; meanwhile in E.coli, it is σ70- dependent[5]. It acts as the master regulator to control the ON/OFF expression of meta-operon on TOL plasmid pWW0[3]. In this meta-operon, XylXYZLTEGFJQKIH genes encode enzymes for the degradation of benzoate and its derivatives, producing intermediate metabolites as carbon sources (Fig.1).


Mechanism

Figure.2 Mechanism of XylS binding to Pm promoter.
Mechanism of transcription activation by XylS at Pm promoter. Step 1: Free DNA. The -10/-35 consensus boxes of σ70-dependent promoter and the two XylS binding sites (D: distal; and P: proximal) are highlighted. The bending angle is supposed to be 35°, centered at XylS proximal binding site. Step 2: A first XylS monomer binds to Pm at the proximal site, shifts the bent center to the DNA sequence between the two XylS binding sites, and increases the bending angle to 50°. Step 3: This conformational change facilitates the binding of a second XylS monomer to the distal site, further increasing the DNA curvature to an overall value of 98°. Step 4: Contacts with RNAP, also probably with the σ-subunit, are established through the α-CTD of RNA polymerase, which dramatically facilitates the open complex formation and transcription initiation.

Tuning of Biosensor



Figure.3(a) Construction of biosensor circuit.
(b) Using a library of constitutive promoters (Pc) to fine-tune the induction ratio of XylS biosensor. Horizontal axis stands for different XylS biosensor circuits with different Pc promoters. These Pc promoters are of different strength to control the expression of XylS. The relative expression strength of these constitutive promoters, J23113, J23109, J23114, J23105, J23106 are 21, 106, 256, 623, and 1185, respectively, according to the Partsregistry. Four kinds of aromatic compounds, namely BzO, 2-MxeBzO, 3-MeBzO and 4-MeBzO, shown with different color intensities, were tested following Test Protocol 1. Vertical axis represents the ON-OFF induction ratio. The Pm/XylS biosensor circuit adopting a weak Pc promoter J23114 performed best throughout the four inducers.

Related Part:
105-XylS-Terminator: https://parts.igem.org/Part:BBa_K1031912
109-XylS-Terminator: https://parts.igem.org/Part:BBa_K1031913
114-XylS-Terminator: https://parts.igem.org/Part:BBa_K1031916


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 32
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 754
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 217

Characterization of Biosensor

ON/OFF test to 78 aromatic compounds

20 compounds showed apparent activation effect with the induction ratios over 20, they are listed as follows: BzO, 2-MeBzO, 3-MeBzO, 4-MeBzO, 2-FBzO, 4-FBzO, 2-ClBzO, 3-ClBzO, 4-ClBzO, 2-BrBzO, 4-BrBzO, 3-IBzO, 3-MeOBzO, SaA, 3-MeOSaA, 4-ClSaA, 5-ClSaA, 3-MeBAD, 3-ClTOL (Fig.4)


Figure.4 (a) The induction ratios of all 78 typical aromatic compounds in the ON/OFF test following Test Protocol 1. XylS biosensor could respond to 24 out of 78 aromatics with the induction ratio higher than 20, mainly benzoate, salicylic and their derivatives.
(b) The aromatics-sensing profile of XylS biosensor is summarized from (a), highlighted in red in the aromatics spectrum. The structure formula of typical inducers are listed around the central spectrum, near their chemical formula.



Dose-response curve to benzoate, salicylic acid and derivatives
Pm/J23114-XylS biosensor circuit was subjected to induction experiments with concentration of inducer ranging at 10 µM, 30µM,100µM, 300µM and 1000µM according to Test Protocol 1. (Fig.5).

Figure.5 (a) Dose-response curves of XylS biosensor induced by benzoate and its derivatives. X-axis stands for concentration gradient of inducers at 10µM, 30µM, 100µM, 300µM and 1000µM. Different colors represent different kinds of inducers. Y-axis shows induction ratios. (b) Dose-response curves of XylS biosensor induced by salicylate and its derivatives. X-axis stands for concentration gradient of inducers at 10µM, 30µM, 100µM, 300µM and 1000µM. Y-axis denotes induction ratios. Different colors denote different kinds of inducers.

Orthogonality of Different Sensor

If the presence of an inducer of biosensor A (not an inducer of biosensor B) doesn’t interfere with the dose response of biosensor B to any of its inducers, and vice versa, we call the B and A biosensors are "orthogonal"; namely, no synergistic/antagonistic effects happen between the inducers of A and B biosensors.(for more details, Chick Here)

SensorHostMain Inducers
XylSPseudomonas putidaBzO 2-MeBzO 3-MeBzO 2,3-MeBzO 3,4-MeBzO
NahRPseudomonas putida4-MeSaA 4-C1SaA 5-C1SaA SaA Aspirin
DmpRPseudomonas sp.600Phl 2-MePhl 3-MePhl 4-MePhl 2-ClPhl
HbpRPseudomonas azelaicao-Phenylphenol 2,6'-DiHydroxybiphenol

Figure.6 Summary of the orthogonality assay to evaluate the synergistic/antagonistic effects between the inducers of 4 representative biosensors.
No synergistic or antagonistic effects between the inducers of 4 representative biosensors (XylS, NahR, HbpR, and DmpR) were observed. For instance, although the sensing profiles of NahR and XylS overlap to some extent, the NahR-specific and XylS-specific inducers proved to be really orthogonal.

We have confirmed the orthogonality among inducers of different biosensors, which is one of the main features we expect for our aromatics-sensing toolkit; this allowed the combination of these biosensors to profile aromatics for the ease of practical applications.

Related Parts:

XylS: https://parts.igem.org/Part:BBa_K1031911 Wiki: http://2013.igem.org/Team:Peking/Project/BioSensors/XylS

NahR: https://parts.igem.org/Part:BBa_K1031610 Wiki: http://2013.igem.org/Team:Peking/Project/BioSensors/NahR

HbpR: https://parts.igem.org/Part:BBa_K1031300 Wiki: http://2013.igem.org/Team:Peking/Project/BioSensors/HbpR

DmpR: http://2013.igem.org/Team:Peking/Project/BioSensors/DmpR


We examined the orthogonality between 4 representative biosensors (Fig.7). The orthogonality test between two biosensors, biosensor I and biosensor II, was performed in the following procedure:

1. A typical inducer A for biosensor I and a typical inducer B for biosensor II were selected.
2. The dose response of biosensor I to inducer A was measured, under the perturbation of inducer B.
3. The dose-response of biosensor II to inducer B was measured, under the perturbation of inducer A.

If biosensor I and biosensor II are orthogonal, the dose response of biosensor I to inducer A should be constant, regardless of the concentrations of inducer B; and the dose response of biosensor II to inducer B should be constant, regardless of the concentrations of inducer A. Namely, for two "orthogonal" biosensors, the perturbation of an unrelated inducer has negligible effect on the dose response of a biosensor to its related inducer (Fig.8).

Figure.7 Orthogonality test assay for inducer A (detected by biosensor I) and inducer B (detected by biosensor II). (a) Biosensor I was added into the test assay. Different mixtures of inducers were added into lane 1, 2, and 3 respectively as listed above. Effect of inducer B upon the dose-response curve of inducer A was tested by comparing the fluorescence intensity of biosensor I among lane 1 ,2, and 3. (b) Biosensor II was added into the test assay. Different mixtures of inducers were added into lane 1, 2, and 3 respectively as listed above. Effect of inducer A upon the dose-response curve of inducer B was tested by comparing the fluorescence intensity of biosensor II among lane 1 ,2, and 3.


Figure.8 Correlation of the inducer B and the dose-response of biosensor I to its inducer A. Each point on the right plot represents a concentration of inducer A. It's x coordinate represents the fluorescence when inducer B is 0 and the y coordinate represents the fluorescence when the cell is exposed to a none-zero concentration of inducer B. If the dose-response of biosensor I is invariant to the concentration of inducer B, the x coordinate of a experimental point should be equal to its y coordinate and the experimental points are supposed to be aligned in a line whose slope is one.


The orthogonality between XylS, NahR, HbpR and DmpR biosensors have been carefully evaluated using the assay discussed above (Fig.7). The data were processed by linear fitting and the slopes of the fitting curves were compared with 1 (Fig.7, Fig.8). The closer the slope was to 1, the more orthogonal the two biosensors were. Results showed that the biosensor pairs, XylS and NahR (Fig.9a, b), XylS and HbpR (Fig.9c, d), NahR and HbpR (Fig.9e, f), XylS and DmpR (Fig.9g, h), NahR and DmpR (Fig.9i, j), and HbpR and DmpR (Fig.9k, l) are all orthogonal, as summarized in Fig.6.

Figure.9 Linear fitting of the data obtained from the orthogonality assay showing that the orthogonality between the 4 representative biosensors. The experiments and data processing were performed as described in Fig. 7 and Fig. 8.The black dashed line denotes slope=1 as the reference line. These fittings showed the orthogonality between biosensors, (a, b) XylS and NahR; (c, d) XylS and HbpR; (e, f) NahR and HbpR, (g, h) XylS and DmpR, (i, j) NahR and DmpR, and (k, l) HbpR and DmpR. The experiment data, linear fitting curves of biosensor, and cognate inducers are in different colors: XylS in red, NahR in green, HbpR in orange and DmpR in dark cyan.

Reference

[1] Kaldalu, N., Toots, U., de Lorenzo, V., & Ustav, M. (2000). Functional domains of the TOL plasmid transcription factor XylS. Journal of bacteriology, 182(4), 1118-1126.
[2] Ramos, J. L., Michan, C., Rojo, F., Dwyer, D., & Timmis, K. (1990). Signal-regulator interactions, genetic analysis of the effector binding site of xyls, the benzoate-activated positive regulator of Pseudomonas TOL plasmid meta-cleavage pathway operon. Journal of molecular biology, 211(2), 373-382.
[3] Ramos, J. L., Marqués, S., & Timmis, K. N. (1997). Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annual Reviews in Microbiology, 51(1), 341-373.
[4] Domínguez-Cuevas, P., Marín, P., Busby, S., Ramos, J. L., & Marqués, S. (2008). Roles of effectors in XylS-dependent transcription activation: intramolecular domain derepression and DNA binding. Journal of bacteriology, 190(9), 3118-3128.
[5] Kaldalu, N., Mandel, T., & Ustav, M. (1996). TOL plasmid transcription factor XylS binds specifically to the Pm operator sequence. Molecular microbiology,20(3), 569-579.