Team:Tokyo Tech/Experiment/3OC12HSL-dependent C4HSL production

From 2014.igem.org

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<h2 class="title">Experiment</h2>
<h2 class="title">Experiment</h2>
                 <span class="meta">3OC12HSL-dependent C4HSL production</span>
                 <span class="meta">3OC12HSL-dependent C4HSL production</span>
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               <p>&nbsp;</p>
               <p>&nbsp;</p>
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              <p align="center"><span class="title-small">Contents</span></p>
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          <p align="left" class="info-24"><a href="#Introduction">1. Introduction </a></p>  
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            <p align="left" class="info-24"><a href="#Summary">2. Summary of the experiments</a></p>
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            <blockquote>
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              <p align="left" class="info-18"><a href="#Summary">2-1. 3OC12HSL-dependent CmR expression</a></p>
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              <p align="left" class="info-18"><a href="#2.2">2-2. 3OC12HSL-dependent C4HSL production</a></p>
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            </blockquote>
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                <p align="left" class="info-24"><a href="#Results">3. Results </a></p>
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                    <blockquote>
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                        <p align="left" class="info-18"><a href="#Results">3.1. 3OC12HSL-depemdent CmR expression</a></p>
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<p align="left" class="info-18"><a href="#3.2">3.2. 3OC12HSL-dependent C4HSL production</a></p>
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                </blockquote>
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                    <p align="left" class="info-24"><a href="#Materials">4. Materials and methods</a></p>
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  <blockquote>
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    <p align="left" class="info-18"><a href="#4.1">4.1. Construction</a></p>
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            <p align="left" class="info-18"><a href="#4.2">4.2. Assay Protocol </a></p>
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            <p align="left" class="info" style="text-indent:40px;"><a href="#4.2.1">4.2.1. 3OC12HSL-depemdent CmR expression</a></p>
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            <p align="left" class="info" style="text-indent:40px;"><a href="#4.2.2">4.2.2. C4HSL-Dependent 3OC12HSL Production Assay</a></p>
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    </blockquote>
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  <p align="left" class="info-24"><a href="#Reference">5. Reference</a></p>
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                <div class="title" style="clear: both;">&nbsp;</div>
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                   <td width="890"><div align="center" class="title-small">3OC12HSL-dependent C4HSL production module</div></td>
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                   <td width="890" class="entry-long"><a name="Introduction" id="Introduction"></a></td>
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                   <td>&nbsp;</td>
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                  <td><h2>1. Introduction</h2></td>
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                   <td><h2>1. Summary of the experiment </h2></td>
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                   <td><p class="info-18">We created a symbiosis of Company and Customer for reproducing the situation in real economy. We used signaling molecules and antibiotics resistance gene, and constructed signal-dependent signal production in our system. In our bank story, we used signaling molecules 3OC12HSL as goods. For construction of the 3OC12HSL-dependent chloramphenicol resistance (CmR) and C4HSL production module, we constructed a new part Plux-CmR-RhlI (<a href="http://parts.igem.org/Part:BBa_K1529797">BBa_K1529797</a>). Plux-CmR-RhlI cell is an engineered E. coli that contains a 3OC12HSL-dependent RhlI generator and a constitutive LuxR generator. As a constitutive LuxR generator, we used Ptet-LuxR. In our bank story, this part reproduces Customer. (Fig. 3-4-1-1.) We confirmed that 3OC12-depedndent growth by measuring optical density, and 3OC12-dependent C4HSL production by using reporter cell.</p>                   </td>
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                   <td><p class="info-18">Construction  of the 3OC12HSL-dependent C4HSL production and chloramphenicol resistance  expression module</p>                  </td>
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                   <td>&nbsp;</td>
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                   <td><p class="info-18">We  created a symbiosis of Company E.coli and Customer E.coli for reproducing the situation  in real economy. We used signaling molecules and antibiotics resistance gene ,and  constructed signal-dependent signal production in our system.</p>                   </td>
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                   <td><div align="center"><img src="fig. 3-4-1-1.png" width="513" height="228" /></div></td>
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                   <td><p class="info-18">For  construction of the 3OC12HSL-dependent chloramphenicol resistance (CmR) and C4HSL  production module, we constructed a new part Plux-CmR-rhlI (BBa_K1529265). Plux-CmR-RhlI cell is an engineered E.coli  that contains a 3OC12HSL-dependent rhlI generator and a constitutive luxR  generator. We constructed a new Biobrick part Plux-CmR-rhlI by combining  Plux-CmR (BBa_K39562) and rhlI (BBa_). As a constitutive luxR generator, we used Pret-luxR (BBa_S0319). In our bank  story, this part is customer.</p>                   </td>
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                   <td><div align="center"><strong>Fig. 3-4-1-1. </strong>Customer&rsquo;s Genetic Circuit</div></td>
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                   <td><p class="head">1-1 3OC12HSL-dependent C4HSL production </p></td>
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                   <td>&nbsp;</td>
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                   <td><p class="info-18">First, we performed a  reporter assay by using rhl reporter cell to characterize the function of 3OC12HSL-dependent C4HSL production. As the negative control of C4HSL production, we prepared C4HSL non-producer cell. C4HSL non-producer cell  contains PlacIq-CmR instead of Plux-CmR-rhlI. The cell of negative control does  not produce C4HSL even in the presence of 3C12HSL.</p></td>
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                   <td><p class="info-18">In the presence of 3OC12HSL, Customer express CmR and RhlI. (C4HSL) (Fig. 3-4-1-2.) (Fig. 3-4-1-3.)</p></td>
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                  <td><div align="center"><img src="fig3-4-1-2.png" width="423" height="265" /></div></td>
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                  <td><div align="center"> <strong>Fig. 3-4-1-2.</strong> 3OC12HSL-dependent CmR expression assay Flow Chart                  </div></td>
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                   <td>&nbsp;</td>
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                  <td><div align="center"><img src="fig3-4-1-3.png" width="500" height="258" /></div></td>
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                  <td><div align="center"><strong>Fig. 3-4-1-3.</strong> 3OC12HSL-dependent C4HSL production assay Flow Chart</div></td>
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                  <td>&nbsp;</td>
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                   <td><p class="info-18">The supernatant of the customer cell were used as the inducer in the reporter assay.</p></td>
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                   <td class="entry-long"><a name="Summary" id="Summary"></a></td>
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                   <td>&nbsp;</td>
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                   <td>&nbsp;</td>
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                  <td><h2>2. Summary of the experiments</h2></td>
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                   <td><p class="info-18">Repoter</p></td>
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                  <td><h1>2-1. 3OC12HSL-dependent CmR expression</h1></td>
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                   <td><p class="info-18">We confirmed the function of 3OC12HSL-dependent CmR expression by measuring optical density of the cell cultures containing chloramphenicol. </p>
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                    <p class="info-18"> In this experiment we prepared  two plasmids, A and B. (See Fig. 3-4-2-1.) Concurrently with 3OC12HSL induction, we added chloramphenicol into the medium containing Customer cell and measured optical density for about 8 h to estimate the concentration of the cell. </p>
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                  <td><div align="center"><img src="fig3-4-2-1.png" width="500" height="184" /></div></td>
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                  <td><div align="center"><strong>Fig. 3-4-2-1.</strong> Plasmids for the experiment of 3OC12HSL-dependent CmR expression
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                  <td><a name="2.2" id="2.2"></a></td>
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                  <td><h1>2-2. 3OC12HSL-dpendent 4CHSL production</h1></td>
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                   <td><p class="info-18">We performed a reporter assay by using reporter cells to characterize the function of 3OC12HSL-dependent C4HSL production. Plux-CmR-RhlI cells contain constitutive luxR generator, and produce C4HSL (RhlI) in the presence of 3OC12HSL. C4HSL is expressed to the culture, so the supernatant of the sender cell contains C4HSL. Reporter cells are incubated in the supernatant of the culture of sender cells. In the presence of C4HSL reporter cells express GFP. We checkefd the fluorescence of reporter cells to confirm of the expression of C4HSL.The expression of the reporter cells were confirmed by Flow Cytometer.</p></td>
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                   <td class="info-18"><div align="center"><img src="fig3-4-2-2.png" width="500" height="176" /></div></td>
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                   <td><div align="center"><strong>Fig. 3-4-2-2.</strong> Plasmids for the experiment of 3OC12HSL-dependent C4HSL production</div></td>
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                   <td><p class="info-18">We prepared four culture conditions as follow.</p></td>
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                   <td><p class="info-18">We prepared four conditions as follow. (PlacIq-CmR cell were used as the negative control.)</p></td>
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                   <td class="info-18">    A) Culture containing  Plux-CmR-RhlI cell with 3OC12HSL induction</td>
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                   <td class="info-18">&nbsp;</td>
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                   <td class="info-18">    B) Culture containing Plux-CmR-RhlI cell without 3OC12HSL induction</td>
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                   <td class="info-18">A-1) Culture containing Plux-CmR-RhlI cell with 3OC12HSL induction</td>
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                   <td class="info-18">    C) Culture containing Plux-CmR cell with 3OC12HSL induction</td>
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                   <td class="info-18">A-2) Culture containing Plux-CmR-RhlI  cell witout induction
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                   <td class="info-18">    D) Culture containing  Plux-CmR cell without 3OC12HSL induction</td>
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                   <td>&nbsp;</td>
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                   <td><p class="info-18">The supernatants of this four different culture were  used as the inducer in the reporter assay. </p></td>
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                   <td class="info-18">B-1) Culture containing PlacIq-CmR cell with 3OC12HSL induction</td>
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                  <td class="info-18">B-2) Culture containing PlacIq-CmR cell without induction</td>
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                   <td><p class="info-18">In the reporter assay, we used a Rhl reporter strain  that contains Ptet-rhlR and Plux-GFP. Also, a reporter cell that expresses GFP  constitutively and a reporter cell that does not express GFP were used as the  positive control and the negative control, respectively.</p></td>
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                   <td class="head">Reporter:</td>
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                   <td><p class="head">1-2  3OC12HSL-dependent growth</p></td>
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                   <td class="info-18">C) Culture containing constitutive RhlR generator and Prhl(RL)-GFP cell</td>
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                   <td><p class="info-18">The cell  which contains Plux-CmR-rhlI can grow in the medium even containing chloramphenicol  .( Chloramphenicol is one of the antibiotics. )
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                   <td>&nbsp;</td>
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                   <td><p class="info-18">After  induction, we added chloramphenicol into the medium and measured optical  density hourly after induction. </p></td>
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                   <td class="info-18">D) Culture containing constitutive RhlR generator and PlacUV5-GFP cell…Positive control</td>
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                   <td><h2>2.  Results</h2></td>
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                   <td class="info-18">E) Culture containing constitutive RhlR generator and Promoter-less-GFP cell…Negative control</td>
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                   <td><p class="head">2-1 3OC12HSL-dependent C4HSL production</p></td>
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                   <td class="entry-long"><a name="Results" id="Results"></a></td>
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                  <td>&nbsp;</td>
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                  <td><h2>3. Results</h2></td>
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                   <td><p class="info-18">We measured GFP  expression in the reporter cell by flow cytometer</p></td>
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                   <td>&nbsp;<a name="3.1" id="3.1"></td>
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                   <td><p class="head">2-2 3OC12HSL-dependent growt</p>                   </td>
+
                   <td><h1>3-1. 3OC12HSL-Depemdent CmR Expression Assay</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">After induction, optical density were measured to estimate the  concentration of the cell.</p></td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-1-1.png"><img src="https://static.igem.org/mediawiki/2014/6/62/Tokyo_Tech_3-1-1.png" alt="" width="450" /></a></div></td>
+
                   <td><p class="info-18">We got results of two type of culture condition which is difference in concentration of chloramphenicol. (Without chloramphenicol and 100 microg / ml)</p>
 +
                  <p class="info-18"><strong>Fig.3-4-3-1.</strong> shows every cell can grow in the absence of chloramphenicol. Conversely, <strong>Fig.3-4-3-2.</strong> shows some cells cannot grow in presence of chloramphenicol.</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><div align="center">Fig. 3-2-1 </div></td>
+
                   <td><div align="center"><img src="fig3-4-3-1.png" width="500" height="279" /></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td><div align="center"><strong>Fig. 3-4-3-1.</strong> 3OC12HSL-Dependent Customer growth in no Cm</div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td><div align="center"></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td><div align="center"><img src="fig3-4-3-2.png" width="604" height="344" /></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td><div align="center"><strong>Fig.3-4-3-2.</strong> 3OC12HSL-dependent Customer growth in 100 microg / mL Cm</div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td><div align="center"></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td><p class="info-18">With induction of 3OC12HSL, the cell containing Plux-CmR-RhlI can grow in the presence of chloramphenicol. However, without induction of 3OC12HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. As a result, only with induction of 3OC12HSL, Plux-CmR-RhlI cell can express CmR and grow well.</p></td>
                 </tr>
                 </tr>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-1-2.png"><img src="https://static.igem.org/mediawiki/2014/b/be/Tokyo_Tech_3-1-2.png" alt="" width="450" /></a></div></td>
+
                   <td><a name="3.2" id="3.2"></a>&nbsp;<a name="3.2" id="3.2"></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><div align="center">Fig. 3-2-2 </div></td>
+
                   <td><h1>3-2. 3OC12HSL-Dependent C4HSL Production Assay</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">As Fig 3-2-shows, the cell containing Plux-CmR-RhlI can grow with induction of 3OC12SL, but can’t  without induction. Plux-CmR-RhlI cell grows more slowly than the positive  control. The amount of CmR is lower than the positive control, Compared Fig  3-2-1 to Fig 3-2-2, With Cm, the cell grow more slowly than without Cm.  geExpression of CmR in Plux-CmR-RhlI depende  on induction by adding 2OC12HSL.          </p>                   </td>
+
                   <td><p class="info-18">As <strong>Fig. 3-4-3-3.</strong> shows, when the reporter cells were incubated in the supernatant of the sender A-1, the fluorescence intensity of the reporter C increased. Comparing the results of used supernatant A-1 and A-2, reporter cell in the supernatant of A-1 (the induced Customer cell&rsquo;s culture) had 95-fold higher fluorescence intensity.</p>
 +
                  <p class="info-18">This result indicates that Company cell produced C4HSL in response to 3OC12HSL induction by the function of Plux-CmR-RhlI.</p>
 +
                  <p class="info-18">From this experiment, we confirmed that a new part Plux-CmR-RhlI synthesized C4HSL (RhlI) as expected.</p></td>
 +
                </tr>
 +
                <tr>
 +
                  <td><div align="center"><img src="fig3-4-3-3.png" width="500" height="320" /></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td><div align="center"><strong>Fig.3-4-3-3.</strong> Customer excretes C4HSL when C12HSL exists</div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><h2>3.  Materials and methods</h2></td>
+
                   <td class="entry-long">&nbsp;<a name="Materials" id="Materials"></a></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="head">3-1 Construction</p></td>
+
                   <td><h2>4. Materials and methods</h2></td>
 +
                </tr>
 +
                <tr>
 +
                  <td>&nbsp;<a name="4.1" id="4.1"></td>
 +
                </tr>
 +
                <tr>
 +
                  <td><h1>4-1 Construction</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18">All  the samples were JM2.300 strain</p></td>
+
                   <td><p class="info-18">All  the samples were JM2.300 strain.</p>                   </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
                   <td><p class="head">-Plasmids</p></td>
                   <td><p class="head">-Plasmids</p></td>
 +
                </tr>
 +
                <tr>
 +
                  <td style="text-indent:0px;"><h3>3OC12HSL-dependent CmR expression</h3></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
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                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="head">3-2 Protocol </p></td>
+
                   <td class="info-18"><div align="left">A. Ptet-GFP-Ptet-RhlR (psB6A1),  Prhl(RL)-CmR-lasI(pSB3K3)</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18" style="text-indent:0px;">3-2-1.  3OC12HSL-dependent C4HSL production assay by using reporter assay</p></td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18"><strong>Prepare the supernatant of the sender cell</strong></p></td>
+
                   <td><div align="center"><img src="fig3-4-4-1.png" width="500" height="86" /></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">1. Grow the colony of sender cell in LB containing antibiotic  O/N at 37°C.</td>
+
                   <td><div align="center"> <strong>Fig. 3-4-4-1.                   </strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB containing  antibiotic and grow the cells at 37°C <br />
+
                   <td><div align="center"></div></td>
-
          until the observed OD590 reaches 0.5.</td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">3. Centrifuge  1mL of the sample at 5000g, RT for 1 minute.</td>
+
                   <td class="info-18">B. Ptet-GFP-Ptet-RhlR (psB6A1)  PlacIq-CmR (pSB3K3) (Positive control)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">4. Suspend the pellet in <u>1 mL of LB containing Ampicillin(50μg/mL)and Kanamycin (30μg/mL)</u></td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">5. Add 30&#181;L of suspension in the following medium.</td>
+
                   <td><div align="center"><img src="untitled.png" width="500" height="86" /></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Add 3&#181;L of 5&#181;M C12HSL to 3mL LB containing Amp and Kan</td>
+
                   <td><div align="center"><strong>Fig.  3-4-4-2.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Add 3&#181;L DMSO to 3 &#181;M of LB containing Amp and Kan</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
-
               
 
                 <tr>
                 <tr>
-
                   <td class="info-18">6. Grow  the samples of sender cell at 37°C for 4 hours.</td>
+
                   <td><h3>3OC12HSL-dependent C4HSL production</h3></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">7. Measure optical density every hour (If optical  density is over 1.0, dilute the cell medium.)</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">8. Centrifuge  sample at 9000g, 4°C for 1minute.Filter sterilize supernatant.</td>
+
                   <td class="info-18" style="text-indent:0px;"><strong>Sender:</strong></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">9. Use  the supernatant in reporter assay</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">&nbsp;</td>
+
                   <td class="info-18">A. Ptet-LuxR-Plac-RFP(pSB6A1)  Plux-CmR-RhlI(pSB3K3)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td><p class="info-18"><strong>Reporter Assay</strong></p></td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">1. Grow the colony of Reporter cell(D~F)  in LB containing antibiotic O/N at 37°C.</td>
+
                   <td><div align="center"><img src="fig3-4-4-3.png" width="500" height="86" /></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB+ antibiotic and grow the cells at 37C until you reach an 0.5 OD590.(fresh  culture)</td>
+
                   <td><div align="center"><strong>Fig3-4-4-3.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">3. Centrifuge  sample at 5000g, 25°C RT for 1 minute. Discard the supernatant.</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">4. Suspended  the sample in 3 mL of LB containing Ampicillin(50μg/mL) and Kanamycin(30μg/mL)</td>
+
                   <td class="info-18">B. Ptet-LuxR-Plac-RFP(pSB6A1)  Plux-CmR(pSB3K3) (Negative control)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">5. Add 30&#181;L of suspension in the following medium.</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Filtrate  of A①+3mL of  LB containing Amp and Kan</td>
+
                   <td><div align="center"><img src="fig3-4-4-4.png" width="500" height="86" /></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Filtrate of A②+3mL of  LB containing Amp and Kan</td>
+
                   <td><div align="center"><strong>Fig. 3-4-4-4.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Filtrate  of B①+3mL of  LB containing Amp and Kan</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Filtrate  of B②+3mL of  LB containing Amp and Kan</td>
+
                   <td class="info-18" style="text-indent:0px;"><strong>Reporter:</strong></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Filtrate  of C①+3mL of  LB containing Amp and Kan</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">          Filtrate  of C②+3mL of  LB containing Amp and Kan</td>
+
                   <td class="info-18"><p align="left" class="info-18">C. Ptet-RhlR(pSB6A1)  Plux-GFP(pSB3K3)</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">          C4HSL+3mL of LB containing Amp and Kan</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">          DMSO +  3mL of LB containing Amp and Kan</td>
+
                   <td><div align="center"><img src="fig3-4-4-5.png" width="500" height="122" /></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">6. Grow the samples of Reporter cell in incubator at 37°C for 4 hours.</td>
+
                   <td><div align="center"><strong>Fig3-3-4-5.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">7. Start  preparing the flow cytometer 1 h before the end of incubation.</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">8. Take  200 microL of the sample, and centrifuge at 9000 Xg, 1 min, 4°C.</td>
+
                   <td class="info-18">D. Ptet-RhlR(pSB6A1)  PlacUV5-GFP(pSB3K3) (Positive control)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">9. Remove  the supernatant by using P1000 pipette.</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">10. Add 1 mL  of filtered PBS (phosphate-buffered saline) and suspend.</td>
+
                   <td><div align="center"><img src="fig3-4-4-6.png" width="500" height="122" /></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">11. Dispense  all of each suspension into a disposable tube through a cell strainer.</td>
+
                   <td><div align="center"><strong>Fig. 3-4-4-6.</strong></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">12. Use  flow cytometer to measure the fluorescence  of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton,  Dickenson and Company).</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">&nbsp;</td>
+
                   <td class="info-18">E. Ptet-RhlR(pSB6A1)  Promoter-less-GFP(pSB3K3) (Negative control)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="head"><p>3-2-2. 3OC12HSL-depemdent CmR expression</p></td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">1. Grow the colony of sender cell in LB containing  antibiotic O/N at 37°C.</td>
+
                   <td><div align="center"><img src="fig3-4-4-7.png" width="500" height="125" /></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB containig antibiotic and grow the cells at 37°C until the observed OD590 reaches  0.5.(fresh culture)</td>
+
                   <td><div align="center">Fig3-4-4-7.</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">3. Centrifuge  1mL of the sample at 5000g, RT for 1 minute.</td>
+
                   <td>&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">4. Suspend the pellet in <u>1 mL of LB containing  Ampicillin(50 microg/mL)and Kanamycin(30 microg/mL)</u></td>
+
                   <td><a name="4.2" id="4.2"></a></td>
 +
                </tr>               
 +
                <tr>
 +
                  <td><h1>4-2. Assay Protocol </h1><a name="4.2.1" id="4.2.1"></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">5. Add 30&#181;L of suspension in the following medium.</td>
+
                   <td><p class="info-18" style="text-indent:0px;"><strong>4-2-1. 3OC12HSL-depemdent CmR expression</strong></p></td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td class="info-18">           Add 3&#181;L of 5&#181;M C12HSL to 3mL LB containing Amp,Kan(concentration  is described upper) and Cm(100 microg /mL)</td>
+
                   <td class="info-18">1. Grow cell in LB containing antibiotic over night at 37°C.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">           Add 3&#181; DMSO to 3mL  of LB containing Amp and Kan</td>
+
                   <td class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB containing antibiotic and grow the cells at 37°C until the observed OD590 reaches 0.5 (→fresh culture)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">6. Grow  the samples of sender cell at 37°C for 4 hours.</td>
+
                   <td class="info-18">3. Add 30 microL of suspension in the following medium.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">7. Measure optical density every hour.  (If optical density is over 1.0, dilute the  cell medium.)</td>
+
                   <td class="info-18">          1) 3 mL of LB containing Amp and Kan + 30 microL C4HSL (final concentration is 500 microM)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td class="info-18">&nbsp;</td>
+
                   <td class="info-18">          2) 3 mL of LB containing Amp and Kan + 30 microL DMSO</td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td><h2>4. Reference</h2></td>
+
                   <td class="info-18">          3) 3 mL of LB containing Amp, Kan and Cm (final concentration is 50mg/mL) + 30 microL C4HSL (final concentration is 500 microM)</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          4) 3 mL of LB containing Amp, Kan and Cm (final concentration is 50mg/mL) + 30 microL DMSO</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">4. Grow the samples of sender cells at 37°C for more than 10 hours.Measure optical density every hour. (If optical density is over 1.0, dilute the cell medium.)</td>
 +
                </tr>
 +
                <tr>
 +
                  <td>&nbsp;<a name="4.2.2" id="4.2.2"></td>
 +
                </tr>
 +
                <tr>
 +
                  <td><p class="info-18" style="text-indent:0px;"><strong>4-2-2. 3OC12HSL-dependent C4HSL production</strong></p></td>
 +
                </tr>
 +
               
 +
                <tr>
 +
                  <td class="info-18">1. Prepare the supernatant of the sender cell</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">2. Grow the colony of sender cell in LB containing antibiotic O/N at 37°C.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">3. Make a 1:100 dilution in 3 mL of fresh LB containing antibiotic and grow the cells at 37°C until the observed OD590 reaches 0.5.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">4. Add 30 microL of the culture containing the cells in the following medium.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          1) Add 30 microL of 500 microM 3OC12HSL to 3 mL LB containing Amp and Kan</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          2) Add 30 microL DMSO to 3 mL LB containing Amp and Kan</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">5 .Grow the samples of sender cell at 37°C for 8 hours.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">6. Centrifuge sample at 9000x g, 4°C for 1minute.Filter sterilize supernatant. (Pore size is 0.22 microm. ) Use this supernatant in reporter assay.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
                   <td class="info-18">&nbsp;</td>
                   <td class="info-18">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18" style="text-indent:0px;"><strong>Reporter Assay</strong></td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">1. Grow the colony of Reporter cell (described upper) in LB containing antibiotic (Amp and Kan) over night at 37°C.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">2. Make a 1:100 dilution in 3 mL of fresh LB+ antibiotic and grow the cells at 37°C until you reach an 0.5 in OD590 (fresh culture).</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">3. Add 30 microL of the culture containing reporter cells in the following medium.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          1) 2.7 mL filtrate of A① +600 microL LB</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          2) 2.7 mL filtrate of A② +600 microL LB</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          3) 2.7 mL filtrate of B① +600 microL LB</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          4) 2.7 mL filtrate of B② +600 microL LB</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          5) 2.7 mL filtrate of C① +600 microL LB</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          6) 2.7 mL filtrate of C② +600 microL LB</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          7) 3 mL LB + 500 microM C4HSL 30 microM (final concentration is 5 microM)</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">          8) 3 mL LB + DMSO 30 microL</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">4. Grow the samples of Reporter cell in incubator at 37°C for 4 hours.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">5. Start preparing the flow cytometer 1 h before the end of incubation.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">6. After incubation, take the sample, and centrifuge at 9000x g, 1 min, 4°C.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">7. Remove the supernatant by using P1000 pipette.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">8. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend. (The ideal of OD is 0.3.)</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">9. Dispense all of each suspension into a disposable tube through a cell strainer.</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">10. Use flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company.)</td>
 +
                </tr>
 +
                <tr>
 +
                  <td>&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td>&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="entry-long"><a name="Reference" id="Reference"></a></td>
 +
                </tr>
 +
                <tr>
 +
                  <td>&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td><h2>5. Reference</h2></td>
 +
                </tr>
 +
                <tr>
 +
                  <td class="info-18">1. Bo Hu <em>et al.</em> (2010) An Environment-Sensitive Synthetic Microbial Ecosystem. PLoS ONE 5(5): e10619</td>
                 </tr>
                 </tr>
               </table>
               </table>
               <p>&nbsp;</p>
               <p>&nbsp;</p>
-
            </div>
+
          </div>
-
            </div>
+
        </div>
  </div>
  </div>
<!-- end #content -->
<!-- end #content -->

Revision as of 12:12, 17 October 2014

Tokyo_Tech

Experiment

3OC12HSL-dependent C4HSL production

 

Contents

1. Introduction

2. Summary of the experiments

2-1. 3OC12HSL-dependent CmR expression

2-2. 3OC12HSL-dependent C4HSL production

3. Results

3.1. 3OC12HSL-depemdent CmR expression

3.2. 3OC12HSL-dependent C4HSL production

4. Materials and methods

4.1. Construction

4.2. Assay Protocol

4.2.1. 3OC12HSL-depemdent CmR expression

4.2.2. C4HSL-Dependent 3OC12HSL Production Assay

5. Reference

 
 

1. Introduction

 

We created a symbiosis of Company and Customer for reproducing the situation in real economy. We used signaling molecules and antibiotics resistance gene, and constructed signal-dependent signal production in our system. In our bank story, we used signaling molecules 3OC12HSL as goods. For construction of the 3OC12HSL-dependent chloramphenicol resistance (CmR) and C4HSL production module, we constructed a new part Plux-CmR-RhlI (BBa_K1529797). Plux-CmR-RhlI cell is an engineered E. coli that contains a 3OC12HSL-dependent RhlI generator and a constitutive LuxR generator. As a constitutive LuxR generator, we used Ptet-LuxR. In our bank story, this part reproduces Customer. (Fig. 3-4-1-1.) We confirmed that 3OC12-depedndent growth by measuring optical density, and 3OC12-dependent C4HSL production by using reporter cell.

 
Fig. 3-4-1-1. Customer’s Genetic Circuit
 

In the presence of 3OC12HSL, Customer express CmR and RhlI. (C4HSL) (Fig. 3-4-1-2.) (Fig. 3-4-1-3.)

Fig. 3-4-1-2. 3OC12HSL-dependent CmR expression assay Flow Chart
 
Fig. 3-4-1-3. 3OC12HSL-dependent C4HSL production assay Flow Chart
 

The supernatant of the customer cell were used as the inducer in the reporter assay.

 
 
 

2. Summary of the experiments

 

2-1. 3OC12HSL-dependent CmR expression

We confirmed the function of 3OC12HSL-dependent CmR expression by measuring optical density of the cell cultures containing chloramphenicol.

 In this experiment we prepared  two plasmids, A and B. (See Fig. 3-4-2-1.) Concurrently with 3OC12HSL induction, we added chloramphenicol into the medium containing Customer cell and measured optical density for about 8 h to estimate the concentration of the cell.

Fig. 3-4-2-1. Plasmids for the experiment of 3OC12HSL-dependent CmR expression

2-2. 3OC12HSL-dpendent 4CHSL production

 

We performed a reporter assay by using reporter cells to characterize the function of 3OC12HSL-dependent C4HSL production. Plux-CmR-RhlI cells contain constitutive luxR generator, and produce C4HSL (RhlI) in the presence of 3OC12HSL. C4HSL is expressed to the culture, so the supernatant of the sender cell contains C4HSL. Reporter cells are incubated in the supernatant of the culture of sender cells. In the presence of C4HSL reporter cells express GFP. We checkefd the fluorescence of reporter cells to confirm of the expression of C4HSL.The expression of the reporter cells were confirmed by Flow Cytometer.

Fig. 3-4-2-2. Plasmids for the experiment of 3OC12HSL-dependent C4HSL production
 

We prepared four conditions as follow. (PlacIq-CmR cell were used as the negative control.)

 
A-1) Culture containing Plux-CmR-RhlI cell with 3OC12HSL induction
A-2) Culture containing Plux-CmR-RhlI cell witout induction
 
B-1) Culture containing PlacIq-CmR cell with 3OC12HSL induction
B-2) Culture containing PlacIq-CmR cell without induction
 
Reporter:
 
C) Culture containing constitutive RhlR generator and Prhl(RL)-GFP cell
 
D) Culture containing constitutive RhlR generator and PlacUV5-GFP cell…Positive control
 
E) Culture containing constitutive RhlR generator and Promoter-less-GFP cell…Negative control
 
 

3. Results

 

3-1. 3OC12HSL-Depemdent CmR Expression Assay

 

We got results of two type of culture condition which is difference in concentration of chloramphenicol. (Without chloramphenicol and 100 microg / ml)

Fig.3-4-3-1. shows every cell can grow in the absence of chloramphenicol. Conversely, Fig.3-4-3-2. shows some cells cannot grow in presence of chloramphenicol.

Fig. 3-4-3-1. 3OC12HSL-Dependent Customer growth in no Cm
Fig.3-4-3-2. 3OC12HSL-dependent Customer growth in 100 microg / mL Cm

With induction of 3OC12HSL, the cell containing Plux-CmR-RhlI can grow in the presence of chloramphenicol. However, without induction of 3OC12HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. As a result, only with induction of 3OC12HSL, Plux-CmR-RhlI cell can express CmR and grow well.

 
 

3-2. 3OC12HSL-Dependent C4HSL Production Assay

 

As Fig. 3-4-3-3. shows, when the reporter cells were incubated in the supernatant of the sender A-1, the fluorescence intensity of the reporter C increased. Comparing the results of used supernatant A-1 and A-2, reporter cell in the supernatant of A-1 (the induced Customer cell’s culture) had 95-fold higher fluorescence intensity.

This result indicates that Company cell produced C4HSL in response to 3OC12HSL induction by the function of Plux-CmR-RhlI.

From this experiment, we confirmed that a new part Plux-CmR-RhlI synthesized C4HSL (RhlI) as expected.

Fig.3-4-3-3. Customer excretes C4HSL when C12HSL exists
 
 
 
 

4. Materials and methods

 

4-1 Construction

-Strain

All the samples were JM2.300 strain.

-Plasmids

3OC12HSL-dependent CmR expression

 
A. Ptet-GFP-Ptet-RhlR (psB6A1), Prhl(RL)-CmR-lasI(pSB3K3)
 
Fig. 3-4-4-1.
B. Ptet-GFP-Ptet-RhlR (psB6A1)  PlacIq-CmR (pSB3K3) (Positive control)
 
Fig. 3-4-4-2.
 

3OC12HSL-dependent C4HSL production

 
Sender:
 
A. Ptet-LuxR-Plac-RFP(pSB6A1)  Plux-CmR-RhlI(pSB3K3)
 
Fig. 3-4-4-3.
 
B. Ptet-LuxR-Plac-RFP(pSB6A1)  Plux-CmR(pSB3K3) (Negative control)
 
Fig. 3-4-4-4.
 
Reporter:
 

C. Ptet-RhlR(pSB6A1)  Plux-GFP(pSB3K3)

 
Fig. 3-3-4-5.
 
D. Ptet-RhlR(pSB6A1)  PlacUV5-GFP(pSB3K3) (Positive control)
 
Fig. 3-4-4-6.
 
E. Ptet-RhlR(pSB6A1)  Promoter-less-GFP(pSB3K3) (Negative control)
 
Fig. 3-4-4-7.
 

4-2. Assay Protocol

4-2-1. 3OC12HSL-depemdent CmR expression

1. Grow cell in LB containing antibiotic over night at 37°C.
2. Make a 1:100 dilution in 3 mL of fresh LB containing antibiotic and grow the cells at 37°C until the observed OD590 reaches 0.5 (→fresh culture)
3. Add 30 microL of suspension in the following medium.
          1) 3 mL of LB containing Amp and Kan + 30 microL C4HSL (final concentration is 500 microM)
          2) 3 mL of LB containing Amp and Kan + 30 microL DMSO
          3) 3 mL of LB containing Amp, Kan and Cm (final concentration is 50mg/mL) + 30 microL C4HSL (final concentration is 500 microM)
          4) 3 mL of LB containing Amp, Kan and Cm (final concentration is 50mg/mL) + 30 microL DMSO
4. Grow the samples of sender cells at 37°C for more than 10 hours.Measure optical density every hour. (If optical density is over 1.0, dilute the cell medium.)
 

4-2-2. 3OC12HSL-dependent C4HSL production

1. Prepare the supernatant of the sender cell
2. Grow the colony of sender cell in LB containing antibiotic O/N at 37°C.
3. Make a 1:100 dilution in 3 mL of fresh LB containing antibiotic and grow the cells at 37°C until the observed OD590 reaches 0.5.
4. Add 30 microL of the culture containing the cells in the following medium.
          1) Add 30 microL of 500 microM 3OC12HSL to 3 mL LB containing Amp and Kan
          2) Add 30 microL DMSO to 3 mL LB containing Amp and Kan
5 .Grow the samples of sender cell at 37°C for 8 hours.
6. Centrifuge sample at 9000x g, 4°C for 1minute.Filter sterilize supernatant. (Pore size is 0.22 microm. ) Use this supernatant in reporter assay.
 
Reporter Assay
1. Grow the colony of Reporter cell (described upper) in LB containing antibiotic (Amp and Kan) over night at 37°C.
2. Make a 1:100 dilution in 3 mL of fresh LB+ antibiotic and grow the cells at 37°C until you reach an 0.5 in OD590 (fresh culture).
3. Add 30 microL of the culture containing reporter cells in the following medium.
          1) 2.7 mL filtrate of A① +600 microL LB
          2) 2.7 mL filtrate of A② +600 microL LB
          3) 2.7 mL filtrate of B① +600 microL LB
          4) 2.7 mL filtrate of B② +600 microL LB
          5) 2.7 mL filtrate of C① +600 microL LB
          6) 2.7 mL filtrate of C② +600 microL LB
          7) 3 mL LB + 500 microM C4HSL 30 microM (final concentration is 5 microM)
          8) 3 mL LB + DMSO 30 microL
4. Grow the samples of Reporter cell in incubator at 37°C for 4 hours.
5. Start preparing the flow cytometer 1 h before the end of incubation.
6. After incubation, take the sample, and centrifuge at 9000x g, 1 min, 4°C.
7. Remove the supernatant by using P1000 pipette.
8. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend. (The ideal of OD is 0.3.)
9. Dispense all of each suspension into a disposable tube through a cell strainer.
10. Use flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company.)
 
 
 

5. Reference

1. Bo Hu et al. (2010) An Environment-Sensitive Synthetic Microbial Ecosystem. PLoS ONE 5(5): e10619