View source for Team:Tokyo Tech/Experiment/C4HSL-dependent growth assay

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      <h1>C4HSL-dependent CmR expression</h1>
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    <h4 class="subtitle"><strong>We have characterized previous parts.</strong></h4>
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     <h2 class="content2">contents</h2>
      <h3 class="link"><a href="#Introduction">1. Introduction</a></h3>
      <h3 class="link"><a href="#Summary">2. Summary of the Experiment</a></h3>
      <h3 class="link"><a href="#Results">3. Results</a></h3>
       <h3 class="link2"><a href="#Result1">3.1. Arabinose dependent FimE expression</a></h3>
       <h3 class="link2"><a href="#Result2">3.2. FLA analysis</a></h3>              
      <h3 class="link"><a href="#Materials">4. Materials and Methods</a></h3>
       <h3 class="link2"><a href="#Const">4.1.  Construction</a></h3>
       <h3 class="link2"><a href="#Protocol">4.2. Assay Protocol</a></h3>
        <h3 class="link3"><a href="#Protol1">4.2.1. C4HSL-dependent CmR expression assay</a></h3>
        <h3 class="link3"><a href="#Protol2">4.2.2. C4HSL-dependent CmR expression assay (With an ssrA tag)</a></h3>
        <h3 class="link3"><a href="#Protol3">4.2.3. Chloramphenicol-dependent Growth Assay with ssrA tag</a></h3>
        <h3 class="link3"><a href="#Protol4">4.2.4. C4HSL-dependent CmR expression assay ([Cm] = 75 microg/mL)</a></h3>
      <h3 class="link"><a href="#Reference">5. Reference</a></h3>
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          <h2 id="Introduction" class="smalltitle">1. Introduction</h2>
　　　　　　<p class="text">We designed a signal-dependent growth system by using signaling molecules and antibiotic resistance gene.  In our prisoner’s dilemma game, our prisoner coli A needs 3OC12HSL to acquire chloramphenicol resistance (CmR).<br>&nbsp;&nbsp; 
	Pcon_<i>rhlR</i>_TT_Plux_CmR (6A1) cell is an engineered E. coli that contains C4HSL-dependent chloramphenicol resistance gene product (CmR) generator and a constitutive RhlR generator. As a constitutive 3OC12HSL production module, we used Plac_<i>lasI</i> (pSB3K3).
	For construction of the C4HSL-dependent chloramphenicol resistance gene product (CmR) and 3OC12HSL production module (Plac_<i>lasI</i>), we constructed an improved parts Pcon_<i>rhlR</i>_TT_Plux_<i>CmRssrA</i> ,<a href="http://parts.igem.org/Part:BBa_K1632023">BBa_K1632023</a>. The C4HSL-dependent growth was confirmed by measuring the optical density.
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　　　　　　    <table width="940 px" border="0px">
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      <td width="940px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/0/0c/Tokyo_Tech_c4HSLsummary1.png" width="450px"/>
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      <h4 align="center" class="fig"><strong>Fig.&nbsp;3-2-1-1.</strong>&nbsp;Matrix of Prisoner <i>coli</i> A</h4>
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　　　　　　<p class="text">We confirmed the function of C4HSL-dependent CmR expression by measuring the optical density of the cultures containing chloramphenicol (Cm) (Fig. 3-2-1-2.). In this experiment we prepared four cells which contain different sets of plasmids, A, B, C, and D (Fig. 3-2-1-2.). C4HSL and chloramphenicol was added into the medium containing the cells. The optical density was measured every hour for eight hours to estimate the concentration of the cell. A, and B are the cooperating and defecting prisoner coli A, respectively. C, and D are the negative control for A, and B, respectively.</p>
　　　　　　    <table width="940 px" border="0px">
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      <h4 align="center" class="fig"><strong>Fig.&nbsp;3-2-2-1.</strong>&nbsp;Plasmids for the experiment of C4HSL dependent CmR expression</h4>
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          <h2 id="Summary" class="smalltitle">2. Summary of the Experiment</h2>
　　　　　　<p class="text"></p>
    <table width="940 px" border="0px">
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      <td width="940px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/d/dd/Tokyo_Tech_arabinosefimB.png" width="800px" />
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      <h4 align="center" class="fig"><strong>Fig.3-4-2-1.</strong>&nbsp;Plasmids for the experiment of FimB dependent fim switch state assay</h4>
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          <h2 id="Results" class="smalltitle">3. Results</h2>
              <h3 id="Result1" class="sub5">3.1. Arabinose dependent FimE expression</h3>
　　　　　　    <p class="text2">私たちは、4種類のarabinose濃度でFimBが働くかどうかを、GFPを用いたレポーターアッセイによって確かめた。
　Figure(図番号) は、default ONのサンプルが、arabinose誘導によって、OFF状態に切り替わった結果を示している。
またFigure(図番号)は、default OFFのサンプルが、arabinose誘導によって、ON状態に切り替わった結果を示している。
Figure(図番号) shows our experimental results of FimB and Fimswitch. From the results of the reporter cell C and D, inversion from ON to OFF and OFF to ON by endogenous proteins are negligible. レポーターセルE,Fの結果から、FImEの発現はヒストグラムの波形にほとんど影響を与えないことがわかる。
以上の2つの結果から、FimBが理想的に両反転を起こしていることがわかる。
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                   <td width="940px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/1/1a/Tokyo_Tech_arabinose_fimB_result1.png" width="800px"/>
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      <h4 align="center" class="fig"><strong>Fig. 3-4-3-1.</strong></h4>
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              <h3 id="Result2" class="sub5">3.2. FLA analysis</h3>
　　　　　　    <p class="text2">写真とシークエンスデータ</p>
          <h2 id="Materials" class="smalltitle">4. Materials and Methods</h2>
              <h3 id="Const" class="sub5">4.1.  Construction</h3>
               <h3 class="sub5">-Strain</h3>
　　　　　　    <p class="text2">All the samples were JM2.300 strain.</p>
              <h3 class="sub5">-Plasmids</h3>





　　　　　　    <p class="text2">(1) Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1) + Plac_lasI (pSB3K3)</p>
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                   <td width="980px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/b/be/Tokyo_Tech_Pcon_rhlR_TT_Plux_CmRssrA_Plac_lasI.png"/>
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      <h4 align="center" class="fig"><strong>Fig. 3-2-4-1.</strong></h4>
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　　　　　　    <p class="text2">(2) Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1) +promoter less_lasI (pSB3K3)</p>
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                   <td width="980px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/2/24/Tokyo_Tech_Pcon_rhlR_TT_Plux_CmRssrA_lasI.png"/>
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      <h4 align="center" class="fig"><strong>Fig. 3-2-4-2.</strong></h4>
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　　　　　　    <p class="text2">(3) Pcon_rhlR_TT_Plux_CmR (pSB6A1) + Plac_lasI (pSB3K3)</p>
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                   <td width="980px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/e/e0/Tokyo_Tech_Pcon_rhlR_TT_CmR_Plac_lasI.png"/>
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      <h4 align="center" class="fig"><strong>Fig. 3-2-4-3.</strong></h4>
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　　　　　　    <p class="text2">(4) Pcon_rhlR_TT_Plux_CmR (pSB6A1) +promoter less_lasI (pSB3K3)</p>
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                   <td width="980px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/3/30/Tokyo_Tech_Pcon_rhlR_TT_Plux_CmR_lasI.png"/>
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      <h4 align="center" class="fig"><strong>Fig. 3-2-4-4.</strong></h4>
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　　　　　　    <p class="text2">(5) Negative control1: Pcon_rhlR_TT_promoter less_CmR (pSB6A1) + Plac_lasI (pSB3K3)</p>
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                   <td width="980px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/e/eb/Tokyo_Tech_Pcon_rhlR_TT_CmR_Plac_lasI.2png.png"/>
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      <h4 align="center" class="fig"><strong>Fig. 3-2-4-5.</strong></h4>
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　　　　　　    <p class="text2">(6) Negative cotrol2:Pcon_rhlR_TT_promoter less_CmR (pSB6A1) +promoter less_lasI (pSB3K3)</p>
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                   <td width="980px"><div align="center"><img src="https://static.igem.org/mediawiki/2015/4/45/Tokyo_Tech_Pcon_rhlR_TT_CmR_lasI.png"/>
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      <h4 align="center" class="fig"><strong>Fig. 3-2-4-6.</strong></h4>
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              <h3 id="Protocol" class="sub5">4.2. Assay Protocol</h3>
               <h3 id="Protol1" class="sub6">4.2.1. C4HSL-dependent CmR expression assay</h3>
                    <p class="text4">
<strong>-samples</strong><br> 
Pcon_rhlR_TT_Plux_CmR (pSB6A1)＋Plac_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_Plux_CmR (pSB6A1)＋Plac_lasI (pSB3K3)#2<br>
Pcon_rhlR_TT_Plux_CmR (pSB6A1)＋ promoter less_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_Plux_CmR (pSB6A1) ＋ promoter less_lasI (pSB3K3)#2<br>
Pcon_rhlR_TT_promoter less_CmR (pSB6A1)＋Plac_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_promoter less_CmR (pSB6A1)＋Plac_lasI (pSB3K3)#2<br>
Pcon_rhlR_TT_promoter less_CmR (pSB6A1)＋promoter less_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_promoter less_CmR (pSB6A1)＋promoter less_lasI (pSB3K3)#2<br>
</p>
                    <p class="text4"><br>
<strong>-Procedure</strong><br>
1. Prepare overnight cultures for the samples in 3 mL LB medium, containing ampicillin (50 microg/mL) and kanamycin (30 microg/mL) at 37°C for 12 hours.<br>
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp (50 microg/mL) and Kan (30 microg/mL) and grow the cells at 37°C until the observed OD590 reaches 0.5.<br>
3. Centrifuge 1 mL of the sample at 5000g, RT for 1 minute.<br>
4. Suspend the pellet in 1mL of LB containing Amp and Kan.<br>
5. Add 30 microL of suspension in the following medium.<br>
&nbsp;&nbsp;&nbsp;①)LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + 50 microM C4HSL (30 microL) + Chloramphenicol (3 microL of 100 microg/mL)<br>
&nbsp;&nbsp;&nbsp;②)LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + DMSO (30 microL) + Chloramphenicol (3 microL of 100 microg/mL)<br>
6. Grow the samples of cells at 37°C for more than 8 hours.<br>
7. Measure optical density every hour. (If the optical density is over 1.0, dilute the cell medium to 1/5.)<br><br>

               <h3 id="Protol2" class="sub6">4.2.2. C4HSL-dependent CmR expression assay (With an ssrA tag)</h3>
                    <p class="text4">
<strong>-samples</strong><br> 
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋Plac_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋Plac_lasI (pSB3K3)#2<br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋promoter less_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋promoter less_lasI (pSB3K3)#2<br>
Pcon_rhlR_TT_Plux_CmR (pSB6A1)＋Plac_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_Plux_CmR (pSB6A1)＋Plac_lasI (pSB3K3)#2<br>
Pcon_rhlR_TT_Plux_CmR (pSB6A1)＋promoter less_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_Plux_CmR (pSB6A1)＋promoter less_lasI (pSB3K3)#2<br>
Pcon_rhlR_TT_promoter less _CmR (pSB6A1)＋Plac_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_promoter less _CmR (pSB6A1)＋Plac_lasI (pSB3K3)#2<br>
Pcon_rhlR_TT_promoter less _CmR (pSB6A1)＋promoter less_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_promoter less _CmR (pSB6A1)＋promoter less_lasI (pSB3K3)#2<br>
<br>
<strong>-Procedure</strong><br>
1. Prepare overnight cultures for the samples in 3 mL LB medium, containing ampicillin (50 microg/mL) and kanamycin (30 microg/mL) at 37°C for 12 hours.<br>
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp (50 microg/mL) and Kan (30 microg/mL) and grow the cells at 37°C until the observed OD590 reaches 0.5.<br>
3. Centrifuge 1 mL of the sample at 5000g, RT for 1 minute.<br>
4. Suspend the pellet in 1mL of LB containing Amp and Kan.<br>
5. Add 30 microL of suspension in the following medium.<br>
&nbsp;&nbsp;&nbsp;①)LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + 50 microM C4HSL (30 microL) + Chloramphenicol (3 microL of 100 microg/mL)<br>
&nbsp;&nbsp;&nbsp;②)LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + DMSO (30 microL) + Chloramphenicol (3 microL of 100 microg/mL)<br>
6. Grow the samples of cells at 37°C for more than 8 hours.<br>
7. Measure optical density every hour. (If the optical density is over 1.0, dilute the cell medium to 1/5.)<br></p>
               <h3 id="Protol3" class="sub6">4.2.3. Chloramphenicol-dependent Growth Assay with ssrA tag</h3>
                    <p class="text4">
<strong>-samples</strong><br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋Plac_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋Plac_lasI (pSB3K3)#2<br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋promoter less_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋promoter less_lasI (pSB3K3)#2<br>
<br><strong>-Procedure</strong><br>
1. Prepare overnight cultures for the samples in 3 mL LB medium, containing ampicillin (50 microg/mL) and kanamycin (30 microg/mL) at 37°C for 12 hours.<br>
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp (50 microg/mL) and Kan (30 microg/mL) and grow the cells at 37°C until the observed OD590 reaches 0.5.<br>
3. Centrifuge 1 mL of the sample at 5000g, RT for 1 minute.<br>
4. Suspend the pellet in 1 mL of LB containing Amp and Kan.<br>
5. Add 30 microL of suspension in the following medium.<br>
&nbsp;&nbsp;&nbsp;①) LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + DMSO (3 microL) + Chloramphenicol (6 microL of 25 microg/mL) + 99.5% ethanol (6 microL)<br>
&nbsp;&nbsp;&nbsp;②) LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + DMSO (3 microL) + Chloramphenicol (9 microL of 25 microg/mL) + 99.5% ethanol (3 microL)<br>
&nbsp;&nbsp;&nbsp;③) LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + DMSO (3 microL) + Chloramphenicol (12 microL of 25 microg/mL)<br>
6. Grow the samples of cells at 37°C for more than 8 hours.<br>
7. Measure the optical density every hour. (If the optical density is over 0.9, dilute the cell medium to 1/5.)<br>
               <h3 id="Protol4" class="sub6">4.2.4. C4HSL-dependent CmR expression assay ([Cm] = 75 microg/mL)</h3>
                    <p class="text4">
<strong>-Samples</strong><br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋Plac_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋Plac_lasI (pSB3K3)#2<br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋promoter less_lasI (pSB3K3)#1<br>
Pcon_rhlR_TT_Plux_CmRssrA (pSB6A1)＋promoter less_lasI (pSB3K3)#2<br>
<br><strong>-Procedure</strong><br>
1. Prepare overnight cultures for the samples in 3 mL LB medium, containing ampicillin (50 microg/mL) and kanamycin (30 microg/mL) at 37°C for 12 hours.<br>
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp (50 microg/mL) and Kan (30 microg/mL) and grow the cells at 37°C until the observed OD590 reaches 0.5.<br>
3. Centrifuge 1 mL of the sample at 5000g, RT for 1 minute.<br>
4. Suspend the pellet in 1mL of LB containing Amp and Kan.<br>
5. Add 30 microL of suspension in the following medium.<br>
&nbsp;&nbsp;&nbsp;①) LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + 50 microM C4HSL (30 microL) + Chloramphenicol (75 microg/mL)<br>
&nbsp;&nbsp;&nbsp;②) LB (3 mL) + antibiotics (Amp 50 microg/mL + Kan 30 microg/mL) + DMSO (30 microL) + Chloramphenicol (75 microg/mL)<br>
6. Grow the samples of cells at 37°C for more than 8 hours.<br>
7. Measure optical density every hour. (If the optical density is over 0.9, dilute the cell medium to 1/5.)<br> 
          <h2 id="Reference" class="smalltitle">6. Reference</h2>
　　　　　　<p class="text">1. Bo Hu <em>et al.</em> (2010) An Environment-Sensitive Synthetic Microbial Ecosystem. PLoS ONE 5(5): e10619</p>
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