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

From 2014.igem.org

(Difference between revisions)
Line 73: Line 73:
                 <p align="left" class="info-24"><a href="#1">1. Introduction </a></p>    
                 <p align="left" class="info-24"><a href="#1">1. Introduction </a></p>    
            <p align="left" class="info-24"><a href="#2">2. Summary of the experiments </a></p>
            <p align="left" class="info-24"><a href="#2">2. Summary of the experiments </a></p>
 +
                                  <p align="left" class="info-18"><a href="#2.1">2.1 C4HSL-dependent CmR expression</a></p>
 +
                                  <p align="left" class="info-18"><a href="#2.2">2.2 C4HSL-dependent 3OC12HSL production </a></p>
                       <p align="left" class="info-24"><a href="#3">3. Results </a></p>
                       <p align="left" class="info-24"><a href="#3">3. Results </a></p>
                       <p align="left" class="info-18"><a href="#3.1">3.1. C4HSL-Dependent  CmR Expression Assay</a></p>
                       <p align="left" class="info-18"><a href="#3.1">3.1. C4HSL-Dependent  CmR Expression Assay</a></p>
Line 94: Line 96:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><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. In our bank story, we used signaling molecules C4HSL as money. For construction of the  C4HSL-dependent chloramphenicol resistance (CmR) and 3OC12HSL production  module, we designed a new part Prhl(RL)-CmR-LasI(<a href="http://parts.igem.org/Part:BBa_K1529302">BBa_K1529302</a>). Prhl(RL)-CmR-LasI cell is an engineered E. coli that contains  a C4HSL-dependent LasI generator and a constitutive RhlR generator. As a constitutive  RhlR generator, we used Ptet-RhlR. In our bank story, this part is Company. (Fig. 3-3-1-1.)</p>                  </td>
+
                   <td colspan="2"><p class="info-18">We designed signal-dependent signal production in our system by using signaling molecules and antibioticss resistance gene. In our bank story, we used signaling molecules C4HSL as money.</p></td>
 +
                </tr>
 +
                  <tr>
 +
                  <td colspan="2"><p class="info-18">For construction of the  C4HSL-dependent chloramphenicol resistance (CmR) and 3OC12HSL production  module, we constructed a new part Prhl(RL)-CmR-LasI(<a href="http://parts.igem.org/Part:BBa_K1529302">BBa_K1529302</a>). Prhl(RL)-CmR-LasI cell is an engineered <i>E. coli</i> that contains  a C4HSL-dependent LasI generator and a constitutive RhlR generator. As a constitutive  RhlR generator, we used Ptet-RhlR. In our bank story, this part imitates the functions of Company. (Fig. 3-3-1-1.) We confirmed that C4HSL-depedent growth by measuring optical density, and C4HSL-dependent 3OC12HSL production by using reporter cell. </p>                  </td>
                 </tr>
                 </tr>
                  
                  
Line 104: Line 109:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig. 3-3-1-1 Company’s Genetic Circuit</div></td>
+
                   <td colspan="2"><div align="center">Fig. 3-3-1-1 Genetic Circuit of Company <i>E. coli</i></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 138: Line 143:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">To  confirm function of Company cell, we performed two kinds of assays. One is C4HSL-Dependent  CmR Expression Assay. In this experiment we prepared four plasmid sets (A, B, C, D) shown  in below. (Fig. 3-3-2-1.) Concurrently with C4HSL  induction, we added chloramphenicol into the medium containing Company cell and  measured optical density for about 8 h to estimate  the concentration of the cell. The other is C4HSL-Dependent 3OC12HSL Production  Assay. In this experiment we prepared three more plasmid sets (E, F, G) shown  in below. (Fig. 3-3-2-1.) First, we  added C4HSL to the culture of sender cell, and induced the expression of LasI. Then,  the supernatants of the culture were used as the  inducer in the reporter assay. We measured the  expression of GFP in reporter cells by flow cytometer.</p>                   </td>
+
                   <td colspan="2"><h1>2-1. C4HSL-dependent CmR expression</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2">&nbsp;</td>
+
                   <td colspan="2"><p class="info-18"> We confirmed the function of C4HSL-dependent CmR expression by measuring optical density of the cell cultures containing chloramphenicol. </a></td>
                 </tr>
                 </tr>
-
                <tr>
+
                  <tr>
-
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-2-1.png"><img src="https://static.igem.org/mediawiki/2014/thumb/5/5f/Tokyo_Tech_3-3-2-1.png/800px-Tokyo_Tech_3-3-2-1.png" width="500" /></a></div></td>
+
                   <td colspan="2"><p class="info-18">In this experiment we prepared three plasmids, A, B and C. (See Fig. 3-4-2-1.) Right after the C4HSL induction, we added chloramphenicol into the medium containing Company cell. We measured optical density for about 8 h to estimate the concentration of the cell.</a>
-
                </tr>
+
</p>                   </td>
-
                <tr>
+
-
                  <td colspan="2"><div align="center">Fig.3-3-2-1.  Constructed plasmids</div></td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 153: Line 156:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">We prepared four conditions as  follow.</p></td>
+
                   <td colspan="2"><h1>2-2. C4HSL-dependent 3OC12HSL production</h1></td>
                 </tr>
                 </tr>
-
                <tr>
+
                  <tr>
-
                   <td colspan="2">&nbsp;</td>
+
                   <td colspan="2"><p class="info-18">We performed a reporter assay by using reporter cells to characterize the function of C4HSL-dependent C4HSL production. Prhl(RL)-CmR-LasI cell containing constitutive RhlR generator expresses LasI and produces 3OC12HSL in the presence of C4HSL. Since 3OC12HSL is excreted to the culture, the supernatant of the sender cell contains 3OC12HSL when the part works as expected. </p></td>
                 </tr>
                 </tr>
-
                <tr>
+
                  <tr>
-
                   <td colspan="2" class="head">Sender: </td>
+
                   <td colspan="2"><p class="info-18"> Reporter cells are incubated in the supernatant of the culture of sender cells. When there are 3OC12HSL in the supernatant, reporter cell expresses GFP. We checked the fluorescence of reporter cells to confirm of the expression of 3OC12HSL.The expression of the reporter cells were measured by Flow Cytometer.</p></td>
-
                </tr>
+
                 </tr><tr>
-
                <tr>
+
-
                  <td colspan="2" class="info-18">&nbsp;</td>
+
-
                </tr>
+
-
                <tr>
+
-
                  <td colspan="2" class="info-18">A-1) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Prhl(RL)-CmR-LasI(pSB3K3) cell with C4HSL induction</td>
+
-
                </tr>
+
-
                <tr>
+
-
                  <td colspan="2" class="info-18">A-2) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Prhl(RL)-CmR-LasI(pSB3K3) cell with DMSO (no induction)</td>
+
-
                 </tr>
+
-
                <tr>
+
                   <td colspan="2">&nbsp;</td>
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">B-1) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and PlacIq-CmR(pSB3K3) cell with C4HSL induction (C4HSL-Dependent CmR Expression  Assay Positive control)</td>
+
                   <td colspan="2"><p class="info-18">We prepared the following conditions for the induction of reporter cells. (Plux-CmR cell was used as the negative control.)</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">B-2) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1) and PlacIq-CmR (pSB3K3) cell with DMSO (no induction) (C4HSL-Dependent CmR Expression  Assay Positive control)</td>
+
                   <td colspan="2"><p class="info-18">(1) Culture containing Prhl(RL)-CmR-lasI cell with C4HSL induction</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2">&nbsp;</td>
+
                   <td colspan="2"><p class="info-18">(2) Culture containing Prhl(RL)-CmR-lasI cell without induction</p></td>
                 </tr>
                 </tr>
-
                <tr>
+
                  <tr>
-
                   <td colspan="2" class="info-18">C-1) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Promoter-less-CmR(pSB3K3) cell with C4HSL induction (C4HSL-Dependent CmR Expression  Assay Negative control)</td>
+
                   <td colspan="2"><p class="info-18">(3) Culture containing Plux-CmR cell with C4HSL induction</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">C-2) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Promoter-less-CmR (pSB3K3) cell with DMSO (no induction) (C4HSL-Dependent CmR Expression  Assay Negative control)</td>
+
                   <td colspan="2"><p class="info-18">(4) Culture containing Plux-CmR cell without induction</p></td>
                 </tr>
                 </tr>
-
                <tr>
+
                  <tr>
-
                   <td colspan="2">&nbsp;</td>
+
                   <td colspan="2"><p class="info-18">(5) 5 microM of artificial C4HSL in LB medium </p></td>
                 </tr>
                 </tr>
-
                <tr>
+
                  <tr>
-
                   <td colspan="2" class="info-18">D-1) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Plux-CmR(pSB3K3) cell with C4HSL induction (C4HSL-Dependent 3OC12HSL Production  Assay Negative control)</td>
+
                   <td colspan="2"><p class="info-18">(6) DMSO in LB medium</p></td>
                 </tr>
                 </tr>
-
                <tr>
+
                  <tr>
-
                  <td colspan="2" class="info-18">D-2) Culture containing Ptet-GFP-Ptet-RhlR(pSB6A1)  and Plux-CmR(pSB3K3) cell with DMSO (no induction) (C4HSL-Dependent 3OC12HSL Production  Assay Negative control)</td>
+
-
                </tr>
+
-
                <tr>
+
                   <td colspan="2">&nbsp;</td>
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="head">Reporter:</td>
+
                   <td colspan="2"><p class="info-18">Reporter</p></td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td colspan="2">&nbsp;</td>
+
                   <td colspan="2" class="info-18">E) The cell containing constitutive LasR generator and Plas-GFP cell</td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">E) Culture containing Ptet-RhlR(pSB6A1) and Prhl(RL)-GFP(pSB3K3)  cell </td>
+
                   <td colspan="2" class="info-18">F) The cell containing constitutive LuxR generator and PlacIq-GFP cell…Positive control</td>
-
                </tr>
+
-
                <tr>
+
-
                  <td colspan="2">&nbsp;</td>
+
-
                </tr>
+
-
                <tr>
+
-
                  <td colspan="2" class="info-18">F) Culture containing Ptet-RhlR(pSB6A1) and PlacIq-GFP(pSB3K3)  cell </td>
+
-
                </tr>
+
-
                <tr>
+
-
                  <td colspan="2">&nbsp;</td>
+
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">G) Culture containing Ptet-RhlR(pSB6A1) and Promoter-less-GFP(pSB3K3)  cell </td>
+
                   <td colspan="2" class="info-18">G) The cell containing constitutive LuxR generator and Promoter-less-GFP cell…Negative control </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 237: Line 221:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><h1>3-1. C4HSL-Dependent CmR Expression Assay</h1></td>
+
                   <td colspan="2"><h1>3-1. C4HSL-dependent CmR expression assay</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">After  induction, optical densities were measured to estimate the concentration of the  cell. We prepared two types of culture conditions which is different in concentration of chloramphenicol. (Without chloramphenicol and 100 microg/ml) </p></td>
+
                   <td colspan="2"><p class="info-18">We tested two type of culture condition which contains different concentration of chloramphenicol(Cm). (0 and 100 microg / mL)</p></td>
 +
                  </tr>
 +
                  <tr>
 +
                  <td colspan="2"><p class="info-18">Fig.3-3-3-1. Fig.3-3-3-2. shows the condition in the absence and presence of chloramphenicol, respectively. </p></td>
 +
                  </tr>
 +
                  <tr>
 +
                  <td colspan="2"><p class="info-18">Fig 3-3-3-1. shows that every cell can grow in the absence of chloramphenicol.
 +
</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 264: Line 255:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">Fig.3-3-3-1.  shows every cell can grow in the absence of chloramphenicol. Conversely, Fig.3-3-3-2.  shows some cells cannot grow in presence of chloramphenicol. With induction of  C4HSL, the cell containing Prhl(RL)-CmR-LuxI can grow in the presence of  chloramphenicol. (The growth curve of the cell is same as the growth curve of  positive control.) However, without induction of C4HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. (The growth curve of  the cell is same as the growth curve of negative control.) As a result, only  with induction of C4HSL, Prhl(RL)-CmR-LuxI (<a href="http://parts.igem.org/Part:BBa_K1529302">BBa_K1529302</a>) cell can  express CmR and grow well.</p></td>
+
                   <td colspan="2"><p class="info-18">On the other hand, in the presence of chloramphenicol, the cell containing Prhl(RL)-CmR-LasI can grow only when induced by C4HSL. Without the induction of C4HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. As a result, we confirmed that Prhl(RL)-CmR-LasI expressed CmR when induced by C4HSL as expected.</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 270: Line 261:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><h1>3-2. C4HSL-Dependent 3OC12HSL Production Assay</h1></td>
+
                   <td colspan="2"><h1>3-2. C4HSL-dependent 3OC12HSL production Assay</h1></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">Four hours after addition of the supernatants from  the culture of sender cells, we measured the expression of GFP in the reporter cells by flow cytometer.</p></td>
+
                   <td colspan="2"><p class="info-18">Fig. 3-3-3-3. shows the fluorescence intensities generated by reporter cells. When the reporter cell E was incubated in the condition (1) (the culture of the induced Company cell), the fluorescence intensity of the reporter cell increased. Comparing the results of condition (1) and (2) reporter cell in the supernatant of (1) had 29-fold higher fluorescence intensity. </p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 279: Line 270:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></td>
+
                   <td colspan="2"><p class="info-18">This result indicates that Company cell produced 3OC12HSL in response to C4HSL induction by the function of Prhl(RL)-CmR-LasI.</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig.  3-3-3-3. C4HSL-Dependent 3OC12HSL Production Assay result</div></td>
+
                   <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2">&nbsp;</td>
+
                   <td colspan="2"><p class="info-18">From this experiment, we confirmed that a new part Prhl(RL)-CmR-LasI synthesized 3OC12HSL (LasI) as expected.</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">As Fig. 3-3-3-3. shows, when the supernatant of condition ??? was  used, the fluorescence intensity of the reporter cell increased. Comparing the  results of condition ??? and ???, reporter cell in the supernatant of induced  Company cell culture had the ???-fold higher fluorescence intensity. This  result indicates that Company cell produced 3OC12HSL in response to C4HSL  induction by the function of Prhl(RL)-CmR-LasI.</p></td>
+
                   <td colspan="2"><div align="center"><a href="#"><img src="" width="500" /></a></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><p class="info-18">From these experiments, we confirmed that a new part  Prhl(RL)-CmR-LasI (<a href="http://parts.igem.org/Part:BBa_K1529302">BBa_K1529302</a>)  synthesized CmR and 3OC12HSL in the presence of C4HSL.</p></td>
+
                   <td colspan="2"><div align="center">Fig. 3-3-3-3. Customer excretes 3OC12HSL when C4HSL exists</div></td>
                 </tr>
                 </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
               
                 <tr>
                 <tr>
                   <td colspan="2">&nbsp;</td>
                   <td colspan="2">&nbsp;</td>
Line 320: Line 315:
                   <td colspan="2"><p class="head">-Plasmids</p></td>
                   <td colspan="2"><p class="head">-Plasmids</p></td>
                 </tr>
                 </tr>
-
                <tr>
+
                  <tr>
-
                   <td colspan="2" class="info-18" style="text-indent:0px;"><strong>Sender:</strong></td>
+
                   <td colspan="2"><p class="info-18">--C4HSL-dependent CmR expression</p></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 327: Line 322:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18"><div align="left">A. Ptet-GFP-Ptet-RhlR (psB6A1),  Prhl(RL)-CmR-lasI(pSB3K3)</div></td>
+
                   <td colspan="2" class="info-18"><div align="left">A. Ptet-GFP-Ptet-RhlR (psB6A1),  Prhl(RL)-CmR-LasI(pSB3K3)</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 342: Line 337:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">B. Ptet-GFP-Ptet-RhlR (psB6A1), PlacIq-CmR (pSB3K3) (C4HSL-Dependent  CmR Expression Assay Positive control)</td>
+
                   <td colspan="2" class="info-18">B. Ptet-GFP-Ptet-RhlR (psB6A1), PlacIq-CmR (pSB3K3)…Positive control</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 357: Line 352:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">C. Ptet-GFP-Ptet-RhlR (pSB6A1), promoter less CmR  (pSB3K3) (C4HSL-Dependent  CmR Expression Assay Negative control)</td>
+
                   <td colspan="2" class="info-18">C. Ptet-GFP-Ptet-RhlR (pSB6A1), promoter less CmR  (pSB3K3)Negative control</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 367: Line 362:
                 <tr>
                 <tr>
                   <td colspan="2"><div align="center">Fig.  3-3-4-3.</div></td>
                   <td colspan="2"><div align="center">Fig.  3-3-4-3.</div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">--C4HSL-dependent 3OC12HSL production</td>
 +
                </tr> 
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 372: Line 373:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">D. Ptet-GFP-Ptet-RhlR (pSB6A1), Plux-CmR (pSB3K3)  (C4HSL-Dependent 3OC12HSL Production Assay Negative control)</td>
+
                   <td colspan="2" class="info-18">Sender</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">A. Ptet-GFP-Ptet-RhlR (pSB6A1), Prhl(RL)-CmR-LasI (pSB3K3)  </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 378: Line 382:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-4.png"><img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Tokyo_Tech_3-3-4-4.png/800px-Tokyo_Tech_3-3-4-4.png" width="500" /></a></div></td>
+
                   <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-1.png"><img src="https://static.igem.org/mediawiki/2014/thumb/5/5e/Tokyo_Tech_3-3-4-1.png/800px-Tokyo_Tech_3-3-4-1.png" width="500" /></a></div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 387: Line 391:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18" style="text-indent:0px;"><strong>Reporter:</strong></td>
+
                   <td colspan="2" class="info-18">D. Ptet-GFP-Ptet-RhlR (pSB6A1), Plux-CmR (pSB3K3)  </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 393: Line 397:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">E. Ptet-luxR (pSB6A1), Plux-GFP (pSB3K3) </td>
+
                  <td colspan="2"><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-3-4-4.png"><img src="https://static.igem.org/mediawiki/2014/thumb/6/62/Tokyo_Tech_3-3-4-4.png/800px-Tokyo_Tech_3-3-4-4.png" width="500" /></a></div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2"><div align="center">Fig.  3-3-4-5.</div></td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2" class="info-18">Reporter</td>
 +
                </tr>
 +
                <tr>
 +
                  <td colspan="2">&nbsp;</td>
 +
                </tr>
 +
                <tr>
 +
                   <td colspan="2" class="info-18">E. Ptrc-LasR (pSB6A1), Plas-GFP (pSB3K3) </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 402: Line 421:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig.  3-3-4-5.</div></td>
+
                   <td colspan="2"><div align="center">Fig.  3-3-4-6図が違う.</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 417: Line 436:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig.  3-3-4-6.</div></td>
+
                   <td colspan="2"><div align="center">Fig.  3-3-4-7.</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 432: Line 451:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2"><div align="center">Fig.  3-3-4-7.</div></td>
+
                   <td colspan="2"><div align="center">Fig.  3-3-4-8.</div></td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 449: Line 468:
                 <tr>
                 <tr>
                   <td colspan="2" 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 colspan="2" 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 />
-
          until the observed OD590 reaches 0.5. If the OD becomes over 0.5, dilute to 0.5 with LB  medium.</td>
+
          until the observed OD590 reaches 0.5.(→fresh culture) </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 482: Line 501:
                  
                  
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">1. Prepare  the supernatant of the sender cell</td>
+
                   <td colspan="2" class="info-18"> Prepare  the supernatant of the sender cell</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">2. Grow the  colony of sender cell in LB containing antibiotic O/N at 37°C.</td>
+
                   <td colspan="2" class="info-18">1. Grow the  colony of sender cell in LB containing antibiotic O/N at 37°C.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" 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.If the OD becomes over 0.5, dilute to o.5 with LB medium.</td>
+
                   <td colspan="2" 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.If the OD becomes over 0.5, dilute to o.5 with LB medium.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">4. Add 30 microL of suspension in the following medium.</td>
+
                   <td colspan="2" class="info-18">3. Add 30 microL of the culture containing the cells in the following medium.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          1) Add 30 microL of 500 microM C4HSL to 3 mL LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          a) Add 15 microL of 10 microM C4HSL to 3 mL LB containing Amp and Kan</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          2) Add 30 microL DMSO to 3 mL of LB containing Amp+Kan</td>
+
                   <td colspan="2" class="info-18">          b) Add 15 microL DMSO to 3 mL of LB containing Amp+Kan</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">5 .Grow the samples of sender cell at 37°C for 4 hours.</td>
+
                   <td colspan="2" class="info-18">4. Grow the samples of sender cell at 37°C for 8 hours.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">6. Measure optical density  every hour. (If optical density is over 1.0, dilute the cell medium to 1/10.)</td>
+
                   <td colspan="2" class="info-18">5. Measure optical density  every hour. (If optical density is over 1.0, dilute the cell medium to 1/10.)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">7. Centrifuge  sample at 9000x g, 4°C for 1minute.Filter sterilize supernatant.</td>
+
                   <td colspan="2" class="info-18">6. Centrifuge  sample at 9000x g, 4°C for 1minute.Filter sterilize supernatant. (Pore size is 0.22 microm.)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">8. Use  the supernatant in reporter assay.</td>
+
                   <td colspan="2" class="info-18">7. Use  the supernatant in reporter assay.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 518: Line 537:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">1. Grow the colony  of  Reporter cell (D~F) in LB containing antibiotic(Amp and  Kan) over night at 37°C.</td>
+
                   <td colspan="2" class="info-18">1. Grow the colony  of  Reporter cell (E~G) in LB containing antibiotic(Amp and  Kan) over night at 37°C.</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
Line 527: Line 546:
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          1) Filtrate  of A①+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          1)2.7 mL filtrate of Aa +300 microL LB </td>
-
                </tr>
+
-
                <tr>
+
-
                  <td colspan="2" class="info-18">          2) Filtrate  of A②+3mL of  LB containing Amp and Kan</td>
+
-
                </tr>
+
-
                <tr>
+
-
                  <td colspan="2" class="info-18">          3) Filtrate  of B①+3mL of LB containing Amp and Kan</td>
+
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          4) Filtrate  of B②+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          2)2.7 mL filtrate of Ab +300 microL LB</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          5) Filtrate  of C①+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          3) 2.7 mL filtrate of Da +300 microL LB </td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          6) Filtrate  of C②+3mL of  LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          4) 2.7 mL filtrate of Db +300 microL LB</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          7) C4HSL+3mL of LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          5)3 mL LB + 500 microM C12HSL 30 microL (final concentration is 5 microM)</td>
                 </tr>
                 </tr>
                 <tr>
                 <tr>
-
                   <td colspan="2" class="info-18">          8) DMSO +  3mL of LB containing Amp and Kan</td>
+
                   <td colspan="2" class="info-18">          6)3 mL LB + DMSO 30 microL </td>
                 </tr>
                 </tr>
 +
               
                 <tr>
                 <tr>
                   <td colspan="2" class="info-18">4. Grow  the samples of Reporter cell in incubator at 37°C for 4 hours.</td>
                   <td colspan="2" class="info-18">4. Grow  the samples of Reporter cell in incubator at 37°C for 4 hours.</td>

Revision as of 19:21, 17 October 2014

Tokyo_Tech

Experiment

C4HSL-dependent 3OC12HSL production

 

Contents

1. Introduction

2. Summary of the experiments

2.1 C4HSL-dependent CmR expression

2.2 C4HSL-dependent 3OC12HSL production

3. Results

3.1. C4HSL-Dependent CmR Expression Assay

3.2. C4HSL-Dependent 3OC12HSL Production Assay

4. Materials and methods

4.1. Construction

4.2. Assay Protocol

4.2.1. C4HSL-Dependent CmR Expression Assay

4.2.2. C4HSL-Dependent 3OC12HSL Production Assay

5. Reference

 
 

1. Introduction

We designed signal-dependent signal production in our system by using signaling molecules and antibioticss resistance gene. In our bank story, we used signaling molecules C4HSL as money.

For construction of the C4HSL-dependent chloramphenicol resistance (CmR) and 3OC12HSL production module, we constructed a new part Prhl(RL)-CmR-LasI(BBa_K1529302). Prhl(RL)-CmR-LasI cell is an engineered E. coli that contains a C4HSL-dependent LasI generator and a constitutive RhlR generator. As a constitutive RhlR generator, we used Ptet-RhlR. In our bank story, this part imitates the functions of Company. (Fig. 3-3-1-1.) We confirmed that C4HSL-depedent growth by measuring optical density, and C4HSL-dependent 3OC12HSL production by using reporter cell.

 
Fig. 3-3-1-1 Genetic Circuit of Company E. coli
 

In order to confirm Company’s dependency on C4HSL, we measured the growth of Company cell and expression of 3OC12HSL in the presence and absence of C4HSL.

 
 
Fig. 3-3-1-2. C4HSL-depemdent CmR expression Assay Flow Chart
Fig. 3-3-1-3. C4HSL-dependent 3OC12HSL
production Assay Flow Chart
 
 

2. Summary of the experiments

2-1. C4HSL-dependent CmR expression

We confirmed the function of C4HSL-dependent CmR expression by measuring optical density of the cell cultures containing chloramphenicol.

In this experiment we prepared three plasmids, A, B and C. (See Fig. 3-4-2-1.) Right after the C4HSL induction, we added chloramphenicol into the medium containing Company cell. We measured optical density for about 8 h to estimate the concentration of the cell.

 

2-2. C4HSL-dependent 3OC12HSL production

We performed a reporter assay by using reporter cells to characterize the function of C4HSL-dependent C4HSL production. Prhl(RL)-CmR-LasI cell containing constitutive RhlR generator expresses LasI and produces 3OC12HSL in the presence of C4HSL. Since 3OC12HSL is excreted to the culture, the supernatant of the sender cell contains 3OC12HSL when the part works as expected.

Reporter cells are incubated in the supernatant of the culture of sender cells. When there are 3OC12HSL in the supernatant, reporter cell expresses GFP. We checked the fluorescence of reporter cells to confirm of the expression of 3OC12HSL.The expression of the reporter cells were measured by Flow Cytometer.

 

We prepared the following conditions for the induction of reporter cells. (Plux-CmR cell was used as the negative control.)

(1) Culture containing Prhl(RL)-CmR-lasI cell with C4HSL induction

(2) Culture containing Prhl(RL)-CmR-lasI cell without induction

(3) Culture containing Plux-CmR cell with C4HSL induction

(4) Culture containing Plux-CmR cell without induction

(5) 5 microM of artificial C4HSL in LB medium

(6) DMSO in LB medium

 

Reporter

E) The cell containing constitutive LasR generator and Plas-GFP cell
F) The cell containing constitutive LuxR generator and PlacIq-GFP cell…Positive control
G) The cell containing constitutive LuxR generator and Promoter-less-GFP cell…Negative control
 
 
 

3. Result

 

3-1. C4HSL-dependent CmR expression assay

We tested two type of culture condition which contains different concentration of chloramphenicol(Cm). (0 and 100 microg / mL)

Fig.3-3-3-1. Fig.3-3-3-2. shows the condition in the absence and presence of chloramphenicol, respectively.

Fig 3-3-3-1. shows that every cell can grow in the absence of chloramphenicol.

 
Fig. 3-3-3-1. C4HSL-Dependent Company Growth in no Cm
 
Fig. 3-3-3-2. C4HSL-Dependent Company Growth in 100 microg/mL Cm
 

On the other hand, in the presence of chloramphenicol, the cell containing Prhl(RL)-CmR-LasI can grow only when induced by C4HSL. Without the induction of C4HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. As a result, we confirmed that Prhl(RL)-CmR-LasI expressed CmR when induced by C4HSL as expected.

 

3-2. C4HSL-dependent 3OC12HSL production Assay

Fig. 3-3-3-3. shows the fluorescence intensities generated by reporter cells. When the reporter cell E was incubated in the condition (1) (the culture of the induced Company cell), the fluorescence intensity of the reporter cell increased. Comparing the results of condition (1) and (2) reporter cell in the supernatant of (1) had 29-fold higher fluorescence intensity.

 

This result indicates that Company cell produced 3OC12HSL in response to C4HSL induction by the function of Prhl(RL)-CmR-LasI.

 

From this experiment, we confirmed that a new part Prhl(RL)-CmR-LasI synthesized 3OC12HSL (LasI) as expected.

Fig. 3-3-3-3. Customer excretes 3OC12HSL when C4HSL exists
 
 
 
 

4. Materials and methods

 

4-1 Construction

-Strain

All the samples were JM2.300 strain.

-Plasmids

--C4HSL-dependent CmR expression

 
A. Ptet-GFP-Ptet-RhlR (psB6A1), Prhl(RL)-CmR-LasI(pSB3K3)
 
Fig. 3-3-4-1.
 
B. Ptet-GFP-Ptet-RhlR (psB6A1), PlacIq-CmR (pSB3K3)…Positive control
 
Fig. 3-3-4-2.
 
C. Ptet-GFP-Ptet-RhlR (pSB6A1), promoter less CmR (pSB3K3)… Negative control
 
Fig. 3-3-4-3.
--C4HSL-dependent 3OC12HSL production
 
 
Sender
A. Ptet-GFP-Ptet-RhlR (pSB6A1), Prhl(RL)-CmR-LasI (pSB3K3)
 
Fig. 3-3-4-4.
 
D. Ptet-GFP-Ptet-RhlR (pSB6A1), Plux-CmR (pSB3K3)
 
Fig. 3-3-4-5.
 
Reporter
 
E. Ptrc-LasR (pSB6A1), Plas-GFP (pSB3K3)
 
Fig. 3-3-4-6図が違う.
 
F. Ptet-LuxR (pSB6A1), PlacIq-GFP (pSB3K3) (Positive control)
 
Fig. 3-3-4-7.
 
G. Ptet-LuxR (pSB6A1), Promoter-less-GFP (pSB3K3) (Negative control)
 
Fig. 3-3-4-8.
 

4-2. Assay Protocol

4-2-1. C4HSL-Dependent CmR Expression Assay

1. Grow the colony of sender cell in LB containing antibiotic O/N 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 + 3 microL C4HSL (5 microM)
          2) 3 mL of LB containing Amp and Kan + 3 microL DMSO
          3) 3 mL of LB containing Amp, Kan and Cm (final concentration is 100 microg/mL)
                   + 30 microL C4HSL (500 microM)
          4) 3 mL of LB containing Amp, Kan and Cm (final concentration is 100 microg/mL) + 30 microL DMSO
4. Grow the samples of sender cells at 37°C for more than 8 hours.
5. Measure optical density every hour. (If optical density is over 1.0, dilute the cell medium to 1/10.)
 

4-2-2. C4HSL-Dependent 3OC12HSL Production Assay

Prepare the supernatant of the sender cell
1. Grow the colony of sender cell in LB containing antibiotic O/N 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.If the OD becomes over 0.5, dilute to o.5 with LB medium.
3. Add 30 microL of the culture containing the cells in the following medium.
          a) Add 15 microL of 10 microM C4HSL to 3 mL LB containing Amp and Kan
          b) Add 15 microL DMSO to 3 mL of LB containing Amp+Kan
4. Grow the samples of sender cell at 37°C for 8 hours.
5. Measure optical density every hour. (If optical density is over 1.0, dilute the cell medium to 1/10.)
6. Centrifuge sample at 9000x g, 4°C for 1minute.Filter sterilize supernatant. (Pore size is 0.22 microm.)
7. Use the supernatant in reporter assay.
 
Reporter Assay
1. Grow the colony of Reporter cell (E~G) 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 suspension in the following medium.
          1)2.7 mL filtrate of Aa +300 microL LB
          2)2.7 mL filtrate of Ab +300 microL LB
          3) 2.7 mL filtrate of Da +300 microL LB
          4) 2.7 mL filtrate of Db +300 microL LB
          5)3 mL LB + 500 microM C12HSL 30 microL (final concentration is 5 microM)
          6)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