Difference between revisions of "Team:Tokyo Tech/Toxin Assay/Queens capricious"

 
(83 intermediate revisions by 4 users not shown)
Line 25: Line 25:
 
     min-width: 880px;
 
     min-width: 880px;
 
     max-width: 1100px;
 
     max-width: 1100px;
 +
}
 +
#main_contents h1{
 +
    padding-bottom: 15px;;
 +
    margin-bottom: 5px;
 
}
 
}
 
.container{
 
.container{
Line 90: Line 94:
 
<div id="main_contents">
 
<div id="main_contents">
 
<div id="page_header" class="container container_top">
 
<div id="page_header" class="container container_top">
<h1 align="center">3-1-4 <span style ="font-style : italic">YafO</span> system assay</h1>
+
<h1 align="center">3-1-3 <span style ="font-style : italic">YafNO</span> system assay</h1>
 
</div><!-- /page_header -->
 
</div><!-- /page_header -->
 
<div id="contents" class="container">
 
<div id="contents" class="container">
Line 101: Line 105:
 
<h3 class="link"><a href="#introduction">1. Introduction</a></h3>
 
<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="#summary">2. Summary of the experiment</a></h3>
                                         <h3 class "link"><a href="#confimling YafO s"><font size="2.7">&nbsp;&nbsp;&nbsp;2-1. Confirming YafO Function as Toxin on Agar plates</font></a></h3>
+
                                         <h3 class "link"><a href="#confimling YafO s_contents"><font size="2.7">&nbsp;&nbsp;&nbsp;2-1. Confirming YafO function as toxin on agar plates</font></a></h3>
                                         <h3 class "link"><a href="#toxin-antitoxin assay s"><font size="2.7">&nbsp;&nbsp;&nbsp;2-2. Toxin-Antitoxin Assay</font></a></h3>
+
                                         <h3 class "link"><a href="#toxin-antitoxin assay s_contents"><font size="2.7">&nbsp;&nbsp;&nbsp;2-2. Toxin-antitoxin assay</font></a></h3>
 
<h3 class="link"><a href="#results">3. Results</a></h3>
 
<h3 class="link"><a href="#results">3. Results</a></h3>
                                         <h3 class "link"><a href="#confimling YafO r"><font size="2.7">&nbsp;&nbsp;&nbsp;3-1. Confirming YafO Function as Toxin on Agar plates</font></a></h3>
+
                                         <h3 class "link"><a href="#confimling YafO r_contents"><font size="2.7">&nbsp;&nbsp;&nbsp;3-1. Confirming YafO function as toxin on agar plates</font></a></h3>
                                         <h3 class "link"><a href="#toxin-antitoxin assay s"><font size="2.7">&nbsp;&nbsp;&nbsp;3-2. Toxin-Antitoxin Assay</font></a></h3>
+
                                         <h3 class "link"><a href="#toxin-antitoxin assay f"><font size="2.7">&nbsp;&nbsp;&nbsp;3-2. Toxin-antitoxin assay</font></a></h3>
 
<h3 class="link"><a href="#discussion">4. Discussion</a></h3>
 
<h3 class="link"><a href="#discussion">4. Discussion</a></h3>
 
<h3 class="link"><a href="#methods">5. Materials and methods</a></h3>
 
<h3 class="link"><a href="#methods">5. Materials and methods</a></h3>
 
<h3 class="link"><a href="#strain"><font size="2.7">&nbsp;&nbsp;&nbsp;5-1. Strain </font></a></h3>
 
<h3 class="link"><a href="#strain"><font size="2.7">&nbsp;&nbsp;&nbsp;5-1. Strain </font></a></h3>
 
<h3 class="link"><a href="#plasmid"><font size="2.7">&nbsp;&nbsp;&nbsp;5-2. Plasmid</font></a></h3>
 
<h3 class="link"><a href="#plasmid"><font size="2.7">&nbsp;&nbsp;&nbsp;5-2. Plasmid</font></a></h3>
                                       <h3 class="link"><a href="#assay"><font size="2.7">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5-2-1. Assay to Confirm YafO function as toxin on agar plates</font></a></h3>
+
                                       <h3 class="link"><a href="#assay"><font size="2.7">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5-2-1. Assay to confirm YafO function as toxin on agar plates</font></a></h3>
                                       <h3 class="link"><a href="#toxin-antitoxin assay m"><font size="2.7">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5-2-2. toxin-antitoxin assay</font></a></h3>
+
                                       <h3 class="link"><a href="#Toxin-antitoxin assay m"><font size="2.7">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5-2-2. Toxin-antitoxin assay</font></a></h3>
<h3 class="link"><a href="#assay protocol"><font size="2.7">&nbsp;&nbsp;&nbsp;5-3. Assay Protocol</font></a></h3>
+
<h3 class="link"><a href="#assay protocol"><font size="2.7">&nbsp;&nbsp;&nbsp;5-3. Assay protocol</font></a></h3>
                                       <h3 class="link"><a href="#confilming YafO a"><font size="2.7">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5-3-1. Confirming YafO function as toxin on agar plate</font></a></h3>
+
                                       <h3 class="link"><a href="#confilming YafO a"><font size="2.7">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5-3-1. Confirming YafO function as toxin on agar plates</font></a></h3>
                                       <h3 class="link"><a href="#toxin-antitoxin assay a"><font size="2.7">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5-3-2. toxin-antitoxin assay</font></a></h3>
+
                                       <h3 class="link"><a href="#toxin-antitoxin assay a"><font size="2.7">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5-3-2. Toxin-antitoxin assay</font></a></h3>
 
<h3 class="link"><a href="#reference">6. Reference</a></h3>
 
<h3 class="link"><a href="#reference">6. Reference</a></h3>
  
Line 127: Line 131:
 
</div><!-- /_header -->
 
</div><!-- /_header -->
 
<div id="introduction_contents" class="container_contents">
 
<div id="introduction_contents" class="container_contents">
<p class="normal_text"> Our project, the story of “Snow White” is constructed based on <i>mazEF</i> system, which is one of toxin-antitoxin (TA) system on <i>E. coli</i> genomic DNA. At the same time, we are interested in other TA systems and we carried out assay using <i>yafNO</i> system.
+
<p class="normal_text"> As described earlier, our project, the story of “Snow White” is constructed based on the <i>mazEF</i> system. At the same time, we are interested in other TA systems and wanted to know which TA system is the most feasible for our project. Here, the assays using the <i>yafNO</i> system was carried out.
  
  
Line 141: Line 145:
 
 
 
<div id="confimling YafO s_contents" class="container_contents">
 
<div id="confimling YafO s_contents" class="container_contents">
                                         <h3><span>2-1. Confirming YafO function as toxin on agar plates</span></h3>
+
                                         <h3><span>2-1. Analyzing YafO function as a toxin on agar plates</span></h3>
 
                          
 
                          
<p class="normal_text"> We first confirmed YafO function by observing formation of colonies on agar plates. This experiment was carried out using <i>E. coli</i> where YafO expression can be induced by arabinose and <i>E. coli</i> without <i>yafO</i> gene. Construction of plasmids used in this experiment is shown as Fig. 2-1-1. We inoculated four types of <i>E. coli</i> differently on agar plates with or without arabinose. <br><br>
+
<p class="normal_text"> We first analyzed YafO function by observing formation of colonies on agar plates. This experiment was carried out using <i>E. coli</i> cells where <i>yafO</i> expression can be induced by arabinose and <i>E. coli</i> cells without <i>yafO</i> gene. The plasmids used in this experiment are shown as Fig. 3-1-3-2-1. We streaked four types of <i>E. coli</i> cells  onto agar plates with or without arabinose. <br><br>
 
+
 
+
  
 
  </p><br>
 
  </p><br>
<div align="center"><img src="https://static.igem.org/mediawiki/2016/8/8b/Construction1.png"height="600"><br></div>
+
<div align="center"><img src="https://static.igem.org/mediawiki/2016/f/f8/Construction11.png"height="600"><br></div>
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 2-1-1. Construction of this experiment </span> <br><br>
+
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-1-3-2-1. Construction of this experiment </span> <br><br>
 
</p></div>
 
</p></div>
                       
+
                     
 
+
</div><!-- /confimling_YafO -->
<h3><span>2-2. Toxin-antitoxin assay</span></h3>
+
</div>
+
 
<div id="toxin-antitoxin assay s_contents" class="container_contents">
 
<div id="toxin-antitoxin assay s_contents" class="container_contents">
<p class="normal_text"> From previous experiment, we confirmed that YafO works as toxin. Next, we confirmed whether the cell growth recovers with antitoxin YafN after inhibition from YafO. Construction of plasmids used in this experiment is shown as Fig. 2-2-1. We prepared <i>E. coli</i> where YafO expression can be induced by arabinose and YafN expression by lactose. As comparisons, we also carried out same experiment with <i>E. coli</i> containing no <i>yafO</i> gene, no <i>yafN</i> gene, or none of them. These <i>E. coli</i> were respectively cultured in media with arabinose in order to express YafO, then IPTG were added to the cultures in order to express YafN. We confirmed YafN function against YafO by measuring turbidity and RFU (relative fluorescence units) of GFP. <br><br>
+
                                        <h3><span>2-2. Toxin-antitoxin assay</span></h3>
 +
<p class="normal_text"> Next, we analyzed whether the growth inhibition caused by YafO can be recovered by the cognate antitoxin YafN. The plasmids used in this experiment are shown in Fig. 3-1-3-2-2. We prepared a transformant where YafO and YafN expression can be induced by arabinose and IPTG, respectively. For comparison, the same experiment were carried out using a transformant containing no <i>yafO</i> gene, no <i>yafN</i> gene or none of them. These <i>E. coli</i> cells were cultured in medium with arabinose to express <i>yafO</i>, and then IPTG was added to the cultures to express <i>yafN</i>.<br><br>
  
 +
</p><br>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2016/7/77/Construction22.png"height="400"><br></div>
 +
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-1-3-2-2. Construction of this experiment </span> <br><br>
  
 
+
</p></div>
</p><br>
+
<div align="center"><img src="https://static.igem.org/mediawiki/2016/d/d7/Construction2.png"height="400"><br></div>
+
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 2-2-1. Construction of this experiment </span> <br><br>
+
</p></div>
+
+
 
</div><!-- /toxin-antitoxin assay s_contents -->
 
</div><!-- /toxin-antitoxin assay s_contents -->
 
</div><!-- /summary -->
 
</div><!-- /summary -->
Line 173: Line 172:
 
<h2><span>3. Results</span></h2>
 
<h2><span>3. Results</span></h2>
 
</div><!-- /_header -->
 
</div><!-- /_header -->
 +
 
<div id="confimling YafO r_contents" class="container_contents">
 
<div id="confimling YafO r_contents" class="container_contents">
                                       <h3><span>3-1. Confirming YafO function as toxin on agar plates</span></h3>
+
                                       <h3><span>3-1. Analyzing YafO function as a toxin on agar plates</span></h3>
 
                          
 
                          
<p class="normal_text">Four types of <i>E. coli</i> shown as Fig. 2-1-1 were inoculated on agar plates with or without 0.2% arabinose, and incubated at 37&deg;C. As a result, <i>E. coli</i> containing plasmid (a) and one containing plasmid (c) didn’t form any colonies, although all types of <i>E. coli</i> formed colonies on agar plate containing no arabinose (A). From this result, cell growth was inhibited by inducing expression of YafO.</p>
+
<p class="normal_text">Four types of transformants shown in Fig. 3-1-3-2-1 were inoculated on agar plates with or without 0.2% arabinose, and these plates were incubated at 37&deg;C. As a result, the transformant containing the plasmid (a) and the one containing plasmid (c) did not form any colonies, although all transformants formed colonies on the agar plate containing no arabinose (A). From this result, it was concluded that cell growth was inhibited by inducing expression of <i>yafO</i>.</p><br><br>
                                <p class="normal_text">Particularly, like E. coli containing plasmid (d), E. coli containing plasmid (c) formed fluorescent colonies on agar plate (A), and didn't form any colonies on agar plate like <i>E. coli</i> containing plasmid (a) on agar plate (B). These results insist that genes on plasmid (c) were working for sure.<br><br>
+
</p>
+
  
+
</p><br>
<div align="center"><img src="https://static.igem.org/mediawiki/2016/9/9a/Result-on-agar-plates.png" height ="450"><br></div>
+
<div align="center"><img src="https://static.igem.org/mediawiki/2016/9/9a/Result-on-agar-plates.png"height ="350"><br></div>
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-1-1. </span>  
+
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-1-3-3-1. Confirming YafO function as a toxin on agar plates</span><br>Each <i>E. coli</i> containing  (a) PBAD &#8208; <i>rbs &#8208; yafO</i> (pSB6A1), (b) PBAD &#8208; <i>rbs</i> (pSB6A1), (c) PBAD &#8208; <i>rbs &#8208; yafO &#8208; tt</i> &#8208; Pcon &#8208; <i>rbs &#8208; gfp</i> (pSB6A1), (d) Pcon &#8208; <i>rbs &#8208; gfp</i> (pSB6A1) were streaked onto LB agar plates (A) (ampicillin 50 microg / mL) and LB agar plates with 0.2% arabinose (B) (ampicillin 50 microg / mL), and incubated at 37°C.
</p></div><br>
+
</p></div>
 
</div><!-- /confimling YafO r_contents -->
 
</div><!-- /confimling YafO r_contents -->
  
  
  
<div id="toxin-antitoxin assay s" class="container_contents">
+
<div id="toxin-antitoxin assay f" class="container_contents">
                                       <h3><span>3-2. toxin-antitoxin assay</span></h3>
+
                                       <h3><span>3-2. Toxin-antitoxin assay</span></h3>
 
                          
 
                          
<p class="normal_text"> Four types of E. coli (shown as Fig. 2-1-1) were inoculated in liquid media, respectively. When turbidity of culture reached 0.03, arabinose was added (final concentration 0.02%) to each culture. After two hours incubation with arabinose, IPTG was also added (final concentration 2 mM). Time-dependent change of RFU and turbidity is shown as Fig. 3-2-1. The graph (A) shows that, even though E. coli containing plasmids (a) has yafN gene, it couldn’t make the cell growth recover, like one containing plasmids (c) (lack yafN gene). Also, from graph (B), no recovery of RFU was shown on E coli containing plasmid (a), and its time-dependent change of RFU was similar to that of turbidity.<br><br>
+
<p class="normal_text"> Four types of transformants (shown as Fig. 3-1-3-2-2) were inoculated in liquid media. When turbidity of culture reached 0.03, arabinose was added (final concentration 0.02%) to each culture. After two hours, IPTG was further added (final concentration 2 mM). Time-dependent change of RFU and turbidity is shown as Fig. 3-1-3-3-2. The graph (A) shows that, even though the transformant containing the plasmids (a) has <i>yafN</i> gene, cell growth was not recovered, like the one containing the plasmids (c) (lacking <i>yafN</i> gene). Also, from the graph (B), no recovery of RFU was shown on the transformant containing the plasmid (a), and its time-dependent change in RFU was similar to that of turbidity.<br><br>
 
</p>  
 
</p>  
 
   
 
   
<div align="center"><img src="https://static.igem.org/mediawiki/2016/0/00/Turbidity-graph.png" height ="450"><br></div>
+
<div align="center"><img src="https://static.igem.org/mediawiki/2016/e/ef/Turbidity-Graph2.png" height ="500"><br></div>
<div align="center"><img src="https://static.igem.org/mediawiki/2016/9/9a/Fluorescence-graph.png" height ="200"><br></div>
+
<div align="center"><img src="https://static.igem.org/mediawiki/2016/b/b7/RFU-Graph2.png" height ="500"><br></div>
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-2-1. </span>  
+
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-1-3-3-2. Toxin-antitoxin assay </span><br>Each culture contained ampicillin (50 microg / mL) and kanamycin (50 microg / mL). Arabinose and IPTG were added at the final concentration of 0.02% and 2 mM, respectively. The graph (A) shows time-dependent change of turbidity, and the graph (B) shows time-dependent change of RFU of GFP.
 
</p></div>
 
</p></div>
<!-- /toxin-antitoxin assay s_contents -->
+
 
 +
</div><!-- /toxin-antitoxin assay s_contents -->
 
</div><!-- /results -->
 
</div><!-- /results -->
  
Line 207: Line 206:
 
</div><!-- /_header -->
 
</div><!-- /_header -->
 
<div id="discussion_contents" class="container_contents">
 
<div id="discussion_contents" class="container_contents">
<p class="normal_text">  From the above result, it was clarified that growth of E. coli cells was repeatedly controlled by expression of mazE. The results of this experiment are very useful in our project, and it is expected to lead to new biotechnological applications.<br>
+
<p class="normal_text">From the above results, it was clarified that growth of <i>E. coli</i> cells was repeatedly controlled by expression of <i>yafO</i>. On the other hand, we could not see YafN work as an antitoxin against YafO in this experiment. After inducing expression of <i>yafO</i> by arabinose, expression of <i>yafN</i> was induced by IPTG, but turbidity and RFU of the culture stayed constant (Fig. 3-1-3-3-2). In the <i>mazEF</i> system, expression of an antitoxin MazE recovered the cell growth caused by a toxin MazF (<a href="https://2016.igem.org/Team:Tokyo_Tech/Toxin_Assay/mazEF_System_Assay">Read This Page</a>). These results insist that the <i>yafNO</i> system has different mechanisms.<br>
On the other hand, we couldn’t see YafN working as antitoxin against yafO in this experiment. After inducing expression of YafO by arabinose, we induced expression of YafN by IPTG, but turbidity and RFU of the culture stayed constant (Fig. 3-2-1). In mazEF system, expression of antitoxin MazE made the cell growth recover from the inhibition by toxin MazF. These results insist that yafNO system has different mechanisms.<br>
+
<p class="normal_text"> From these results, the <i>yafNO</i> system could not implement “Stop & go” of <i>E. coli</i> cell growth.<br>
From these results, yafNO system couldn’t carry out “Stop&go” of E. coli cell growth, and we considered that this system can’t be treated the same as mazEF system, which is the basis of our project.<br>
+
  
 
</p>
 
</p>
Line 217: Line 215:
 
<div id="methods" class="container">
 
<div id="methods" class="container">
 
<div id="methods_header" class="container_header">
 
<div id="methods_header" class="container_header">
<h2><span>5. Materials and Methods</span></h2>
+
<h2><span>5. Materials and methods</span></h2>
 
</div><!-- /_header -->
 
</div><!-- /_header -->
 
<div id="methods_contents" class="container_contents">
 
<div id="methods_contents" class="container_contents">
<div id="construction">
+
<div class="construction">
<div id="construction_header">
+
<div id="strain" class="construction_header">
 
<h3><span>5-1. Strain</span></h3>
 
<h3><span>5-1. Strain</span></h3>
 
</div><!-- /_header -->
 
</div><!-- /_header -->
<div id="construction_contents">
+
<div class="construction_contents">
 
<p class="normal_text"> All the samples were XL1-Blue strain.<br>
 
<p class="normal_text"> All the samples were XL1-Blue strain.<br>
 
+
</div><!-- /construction_contents -->
                                 <div id="construction_header">
+
                                 <div id="plasmid" class="construction_header">
 
<h3><span>5-2. Plasmid</span></h3>
 
<h3><span>5-2. Plasmid</span></h3>
 
</div><!-- /_header -->
 
</div><!-- /_header -->
<div id="construction_contents">
+
<div class="construction_contents">
                                 <div id="construction_header">
+
</div>
<h4><span>5-2-1. Assay to Confirm YafO function as toxin on agar plates</span></h4>
+
                                 <div id="assay" class="construction_header">
 +
<h4><span>5-2-1. Assay to confirm YafO function as toxin on agar plates</span></h4>
 
</div><!-- /_header -->
 
</div><!-- /_header -->
 +
 +
<div class="construction_contents">
 
<p class="normal_text"><br>
 
<p class="normal_text"><br>
  (a) PBAD_rbs_yafO (pSB6A1)<br>
+
  (a) PBAD &#8208; <i>rbs &#8208; yafO</i> (pSB6A1)<br>
  (b) PBAD_rbs (pSB6A1)<br>
+
  (b) PBAD &#8208; <i>rbs</i> (pSB6A1)<br>
  (c) PBAD_rbs_yafO_tt_Ptet_rbs_gfp (pSB6A1)<br>
+
  (c) PBAD &#8208; <i>rbs &#8208; yafO &#8208; tt</i> &#8208; Ptet &#8208; <i>rbs &#8208; gfp</i> (pSB6A1)<br>
  (d) Ptet_rbs_gfp (pSB6A1)<br><br>
+
  (d) Ptet &#8208; <i>rbs &#8208; gfp</i> (pSB6A1)<br>
 +
<p class="normal_text">PBAD &#8208; <i>rbs</i> &#8208; <i>yafO</i> (<a href="http://parts.igem.org/Part:BBa_K1949032">BBa_K1949032</a>), PBAD (<a href="http://parts.igem.org/Part:BBa_I0500">BBa_I0500</a>), <i>rbs</i> (<a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a>), PBAD &#8208; <i>rbs</i> &#8208; <i>yafO</i> &#8208; <i>tt</i> &#8208; Ptet &#8208; <i>rbs</i> &#8208; <i>gfp</i> (<a href="http://parts.igem.org/Part:BBa_K1949033">BBa_K1949033</a>), Ptet (<a href="http://parts.igem.org/Part:BBa_R0040">BBa_R0040</a>), <i>gfp</i> (<a href="http://parts.igem.org/Part:BBa_E0040">BBa_E0040</a>)
 +
                                        </p><br><br>
  
<div id="construction_contents">
+
</div>
                                 <div id="construction_header">
+
                                 <div id="Toxin-antitoxin assay m" class="construction_header">
<h4><span>5-2-2. toxin-antitoxin assay</span></h4>
+
<h4><span>5-2-2. Toxin-antitoxin assay</span></h4>
 
</div><!-- /_header -->
 
</div><!-- /_header -->
 +
 +
<div class="construction_contents">
 
<p class="normal_text"><br>
 
<p class="normal_text"><br>
(a) PBAD_rbs_yafO_tt_Ptet_rbs_gfp (pSB6A1) , Plac_rbs_yafN (pSB3K3)<br>
+
(a) PBAD &#8208; <i>rbs &#8208; yafO &#8208; tt</i> &#8208; Ptet &#8208; <i>rbs &#8208; gfp</i> (pSB6A1) , Plac &#8208; <i>rbs &#8208; yafN</i> (pSB3K3)<br>
(b) Ptet_rbs_gfp (pSB6A1), Plac_rbs_yafN (pSB3K3)<br>
+
(b) Ptet &#8208; <i>rbs &#8208; gfp</i> (pSB6A1), Plac &#8208; <i>rbs &#8208; yafN</i> (pSB3K3)<br>
(c) PBAD_rbs_yafO_tt_Ptet_rbs_gfp (pSB6A1), Plac_rbs (pSB3K3)<br>
+
(c) PBAD &#8208; <i>rbs &#8208; yafO &#8208; tt</i> &#8208; Ptet &#8208; <i>rbs &#8208; gfp</i> (pSB6A1), Plac &#8208; <i>rbs</i> (pSB3K3)<br>
(d) Ptet_rbs_gfp (pSB6A1), Plac_rbs (pSB3K3)<br><br>
+
(d) Ptet &#8208; <i>rbs &#8208; gfp</i> (pSB6A1), Plac &#8208; <i>rbs</i> (pSB3K3)<br>
 +
<p class="normal_text">PBAD &#8208; <i>rbs</i> &#8208; <i>yafO</i> &#8208; <i>tt</i> &#8208; Ptet &#8208; <i>rbs</i> &#8208; <i>gfp</i> (<a href="http://parts.igem.org/Part:BBa_K1949033">BBa_K1949033</a>), Plac &#8208; <i>rbs</i> &#8208; <i>yafN</i> (<a href="http://parts.igem.org/Part:BBa_K1949022 ">BBa_K1949022</a>), Ptet (<a href="http://parts.igem.org/Part:BBa_R0040">BBa_R0040</a>), <i>rbs</i> (<a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a>), <i>gfp</i> (<a href="http://parts.igem.org/Part:BBa_E0040">BBa_E0040</a>), Plac (<a href="http://parts.igem.org/Part:BBa_J04500">BBa_J04500</a>)
 +
                                        </p><br><br>
  
 
+
</div>
                                 <div id="construction_header">
+
                                 <div id="assay protocol" class="construction_header">
<h3><span>5-3. Assay Protocol</span></h3>
+
<h3><span>5-3. Assay protocol</span></h3>
 
</div><!-- /_header -->
 
</div><!-- /_header -->
<div id="construction_contents">
+
<div class="construction_contents">
                                 <div id="construction_header">
+
</div>
 +
                                 <div id="confilming YafO a" class="construction_header">
 
<h4><span>5-3-1. Confirming YafO function as toxin on agar plate</span></h4>
 
<h4><span>5-3-1. Confirming YafO function as toxin on agar plate</span></h4>
 
</div><!-- /_header -->
 
</div><!-- /_header -->
 +
<div class="construction_contents">
 
<p class="normal_text"><br>
 
<p class="normal_text"><br>
1) Inoculate each E. coli on LB agar plates containing ampicillin (50 microg/mL) with or without 0.2% arabinose, and incubate at 37°C.<br>
+
1) Inoculate each <i>E. coli</i> on LB agar plates containing ampicillin (50 microg / mL) with or without 0.2% arabinose, and incubate at 37°C.<br><br>
2) Observe whether colonies were formed on the agar plates.<br><br>
+
2) Observe whether colonies were formed on the agar plates.<br><br>
 
+
</div>
 
<div id="construction_contents">
 
<div id="construction_contents">
                                 <div id="construction_header">
+
</div>
<h4><span>5-3-2. toxin-antitoxin assay</span></h4>
+
                                 <div id="toxin-antitoxin assay a">
 +
<h4><span>5-3-1. toxin-antitoxin assay</span></h4>
 
</div><!-- /_header -->
 
</div><!-- /_header -->
 +
<div class="construction_contents">
 
<p class="normal_text"><br>
 
<p class="normal_text"><br>
1. Pre-culture<br>
+
1. Pre-culture<br>
1) Scrape E. coli colonies on a master plate and inoculate them in LB media containing ampicillin (50 microg/mL) and kanamycin (50 microg/mL).<br>
+
<p class="normal_text"> 1) Scrape <i>E. coli</i> colonies on a master plate and inoculate them in LB media containing<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ampicillin (50 microg/mL) and kanamycin (50 microg/mL).</p><br>
2) Incubate the samples with shaking for 12 h.<br>
+
<p class="normal_text"> 2) Incubate the samples with shaking for 12 h.</p><br>
2. Incubation and Assay<br>
+
<!-- /_header -->
1) Measure the turbidity of the pre-cultures.<br>
+
<p class="normal_text"><br>
2) Dilute the pre-cultures to 1/30 with LB media containing 4 mL ampicillin and kanamycin. <br>
+
2. Incubation and assay<br>
3) Incubate the samples with shaking.<br>
+
<p class="normal_text"> 1) Measure the turbidity of the pre-cultures.</p><br>
4) Add arabinose so that the final concentration becomes 0.02% at 0 h when the turbidity reaches 0.03.<br>
+
<p class="normal_text"> 2) Dilute the pre-cultures to 1/30 with LB medium containing 4 mL ampicillin and<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; kanamycin. </p><br>
5) Measure the turbidity and RFU of GFP at appropriate time. RFU of GFP was measured using wavelength 490 nm for excitation and wavelength 525 nm for measurement.<br>
+
<p class="normal_text"> 3) Incubate the samples with shaking.</p><br>
6) Add IPTG so that final concentration becomes 2 mmol/L after 2 h arabinose was added.<br>
+
<p class="normal_text"> 4) Add arabinose so that the final concentration becomes 0.02% at 0 h when the turbidity<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; reaches 0.03.</p><br>
7) Measure the turbidity and RFU of GFP at appropriate time. In this experiment, Infinite® m200 PRO was used for measuring turbidity and RFU of GFP.<br><br>
+
<p class="normal_text"> 5) Measure the turbidity and RFU of GFP at appropriate time. RFU of GFP was measured<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; using wavelength 490 nm for excitation and wavelength 525 nm for measurement.</p><br>
 
+
<p class="normal_text"> 6) Add IPTG so that final concentration becomes 2 mM after 2 h arabinose was added.</p><br>
 +
<p class="normal_text"> 7) Measure the turbidity and RFU of GFP at appropriate time. In this experiment, Infinite®<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; m200 PRO was used for measuring turbidity and RFU of GFP.<br><br>
  
 
</p>
 
</p>
 +
</div>
 +
</div><!-- /construction -->
 
</div><!-- /methods_contents -->
 
</div><!-- /methods_contents -->
 
</div><!-- /methods -->
 
</div><!-- /methods -->
Line 290: Line 304:
 
</div><!-- /_header -->
 
</div><!-- /_header -->
 
<div id="reference_contents" class="container_contents">
 
<div id="reference_contents" class="container_contents">
<p class="normal_text">
+
<p class="normal_text"><br>
[1] Yonglong Zhang, Yoshihiro Yamaguchi, and Masayori Inoue. Characterization of YafO, an Escherichia coli Toxin. J Biol Chem 2009 Sep;284(38): 25522-25531.<br><br>
+
[1] Yonglong Zhang, Yoshihiro Yamaguchi, and Masayori Inoue. Characterization of YafO, an <i>Escherichia coli</i> Toxin. J Biol Chem 2009 Sep;284(38): 25522-25531.<br><br>
  
[2] Mikkel Christensen Dalsgaard, Mikkel Girke Jørgensen and Kenn Gerdes. Three new RelE-homologous mRNA interferases of Escherichia coli differentially induced by environmental stresses. Mol Microbiol 2010 Jan;75(2): 333-348.<br><br>
+
[2] Mikkel Christensen Dalsgaard, Mikkel Girke Jørgensen and Kenn Gerdes. Three new RelE-homologous mRNA interferases of <i>Escherichia coli</i> differentially induced by environmental stresses. Mol Microbiol 2010 Jan;75(2): 333-348.<br><br>
  
 
[3] Larissa A. Singletary, Janet L. Gibson, Elizabeth J. Tanner, Gregory J. McKenzie, Peter L. Lee, Caleb Gonzalez, and Susan M. Rosenberg. An SOS-Regulated Type 2 Toxin-Antitoxin System.  J Bacteriol 2009 Dec;191(24): 7456-7465.<br><br>
 
[3] Larissa A. Singletary, Janet L. Gibson, Elizabeth J. Tanner, Gregory J. McKenzie, Peter L. Lee, Caleb Gonzalez, and Susan M. Rosenberg. An SOS-Regulated Type 2 Toxin-Antitoxin System.  J Bacteriol 2009 Dec;191(24): 7456-7465.<br><br>
Line 304: Line 318:
 
</div><!-- /reference -->
 
</div><!-- /reference -->
  
 +
<div id="next_page" class="container">
 +
<div id="next_page_contents" class="container_contents">
 +
<p class="normal_text">Jump to <a href="https://2016.igem.org/Team:Tokyo_Tech/AHL_Assay/AHL_Reporter_Assay">AHL reporter assay</a> page.</p>
 +
<p class="normal_text">Jump to <a href="https://2016.igem.org/Team:Tokyo_Tech">Home</a>.</p>
 +
 +
</div><!-- /next_page_contents -->
 +
</div><!-- /next_page -->
 +
 +
</div><!-- /main_contents -->
  
 
</body>
 
</body>
 
</html>
 
</html>

Latest revision as of 12:02, 6 November 2016

1. Introduction

As described earlier, our project, the story of “Snow White” is constructed based on the mazEF system. At the same time, we are interested in other TA systems and wanted to know which TA system is the most feasible for our project. Here, the assays using the yafNO system was carried out.

2. Summary of the experiment

2-1. Analyzing YafO function as a toxin on agar plates

We first analyzed YafO function by observing formation of colonies on agar plates. This experiment was carried out using E. coli cells where yafO expression can be induced by arabinose and E. coli cells without yafO gene. The plasmids used in this experiment are shown as Fig. 3-1-3-2-1. We streaked four types of E. coli cells onto agar plates with or without arabinose.



Fig. 3-1-3-2-1. Construction of this experiment

2-2. Toxin-antitoxin assay

Next, we analyzed whether the growth inhibition caused by YafO can be recovered by the cognate antitoxin YafN. The plasmids used in this experiment are shown in Fig. 3-1-3-2-2. We prepared a transformant where YafO and YafN expression can be induced by arabinose and IPTG, respectively. For comparison, the same experiment were carried out using a transformant containing no yafO gene, no yafN gene or none of them. These E. coli cells were cultured in medium with arabinose to express yafO, and then IPTG was added to the cultures to express yafN.



Fig. 3-1-3-2-2. Construction of this experiment

3. Results

3-1. Analyzing YafO function as a toxin on agar plates

Four types of transformants shown in Fig. 3-1-3-2-1 were inoculated on agar plates with or without 0.2% arabinose, and these plates were incubated at 37°C. As a result, the transformant containing the plasmid (a) and the one containing plasmid (c) did not form any colonies, although all transformants formed colonies on the agar plate containing no arabinose (A). From this result, it was concluded that cell growth was inhibited by inducing expression of yafO.





Fig. 3-1-3-3-1. Confirming YafO function as a toxin on agar plates
Each E. coli containing (a) PBAD ‐ rbs ‐ yafO (pSB6A1), (b) PBAD ‐ rbs (pSB6A1), (c) PBAD ‐ rbs ‐ yafO ‐ tt ‐ Pcon ‐ rbs ‐ gfp (pSB6A1), (d) Pcon ‐ rbs ‐ gfp (pSB6A1) were streaked onto LB agar plates (A) (ampicillin 50 microg / mL) and LB agar plates with 0.2% arabinose (B) (ampicillin 50 microg / mL), and incubated at 37°C.

3-2. Toxin-antitoxin assay

Four types of transformants (shown as Fig. 3-1-3-2-2) were inoculated in liquid media. When turbidity of culture reached 0.03, arabinose was added (final concentration 0.02%) to each culture. After two hours, IPTG was further added (final concentration 2 mM). Time-dependent change of RFU and turbidity is shown as Fig. 3-1-3-3-2. The graph (A) shows that, even though the transformant containing the plasmids (a) has yafN gene, cell growth was not recovered, like the one containing the plasmids (c) (lacking yafN gene). Also, from the graph (B), no recovery of RFU was shown on the transformant containing the plasmid (a), and its time-dependent change in RFU was similar to that of turbidity.



Fig. 3-1-3-3-2. Toxin-antitoxin assay
Each culture contained ampicillin (50 microg / mL) and kanamycin (50 microg / mL). Arabinose and IPTG were added at the final concentration of 0.02% and 2 mM, respectively. The graph (A) shows time-dependent change of turbidity, and the graph (B) shows time-dependent change of RFU of GFP.

4. Discussion

From the above results, it was clarified that growth of E. coli cells was repeatedly controlled by expression of yafO. On the other hand, we could not see YafN work as an antitoxin against YafO in this experiment. After inducing expression of yafO by arabinose, expression of yafN was induced by IPTG, but turbidity and RFU of the culture stayed constant (Fig. 3-1-3-3-2). In the mazEF system, expression of an antitoxin MazE recovered the cell growth caused by a toxin MazF (Read This Page). These results insist that the yafNO system has different mechanisms.

From these results, the yafNO system could not implement “Stop & go” of E. coli cell growth.

5. Materials and methods

5-1. Strain

All the samples were XL1-Blue strain.

5-2. Plasmid

5-2-1. Assay to confirm YafO function as toxin on agar plates


(a) PBAD ‐ rbs ‐ yafO (pSB6A1)
(b) PBAD ‐ rbs (pSB6A1)
(c) PBAD ‐ rbs ‐ yafO ‐ tt ‐ Ptet ‐ rbs ‐ gfp (pSB6A1)
(d) Ptet ‐ rbs ‐ gfp (pSB6A1)

PBAD ‐ rbsyafO (BBa_K1949032), PBAD (BBa_I0500), rbs (BBa_B0034), PBAD ‐ rbsyafOtt ‐ Ptet ‐ rbsgfp (BBa_K1949033), Ptet (BBa_R0040), gfp (BBa_E0040)



5-2-2. Toxin-antitoxin assay


(a) PBAD ‐ rbs ‐ yafO ‐ tt ‐ Ptet ‐ rbs ‐ gfp (pSB6A1) , Plac ‐ rbs ‐ yafN (pSB3K3)
(b) Ptet ‐ rbs ‐ gfp (pSB6A1), Plac ‐ rbs ‐ yafN (pSB3K3)
(c) PBAD ‐ rbs ‐ yafO ‐ tt ‐ Ptet ‐ rbs ‐ gfp (pSB6A1), Plac ‐ rbs (pSB3K3)
(d) Ptet ‐ rbs ‐ gfp (pSB6A1), Plac ‐ rbs (pSB3K3)

PBAD ‐ rbsyafOtt ‐ Ptet ‐ rbsgfp (BBa_K1949033), Plac ‐ rbsyafN (BBa_K1949022), Ptet (BBa_R0040), rbs (BBa_B0034), gfp (BBa_E0040), Plac (BBa_J04500)



5-3. Assay protocol

5-3-1. Confirming YafO function as toxin on agar plate


1) Inoculate each E. coli on LB agar plates containing ampicillin (50 microg / mL) with or without 0.2% arabinose, and incubate at 37°C.

2) Observe whether colonies were formed on the agar plates.

5-3-1. toxin-antitoxin assay


1. Pre-culture

1) Scrape E. coli colonies on a master plate and inoculate them in LB media containing
        ampicillin (50 microg/mL) and kanamycin (50 microg/mL).


2) Incubate the samples with shaking for 12 h.



2. Incubation and assay

1) Measure the turbidity of the pre-cultures.


2) Dilute the pre-cultures to 1/30 with LB medium containing 4 mL ampicillin and
       kanamycin.


3) Incubate the samples with shaking.


4) Add arabinose so that the final concentration becomes 0.02% at 0 h when the turbidity
       reaches 0.03.


5) Measure the turbidity and RFU of GFP at appropriate time. RFU of GFP was measured
       using wavelength 490 nm for excitation and wavelength 525 nm for measurement.


6) Add IPTG so that final concentration becomes 2 mM after 2 h arabinose was added.


7) Measure the turbidity and RFU of GFP at appropriate time. In this experiment, Infinite®
       m200 PRO was used for measuring turbidity and RFU of GFP.

6. Reference


[1] Yonglong Zhang, Yoshihiro Yamaguchi, and Masayori Inoue. Characterization of YafO, an Escherichia coli Toxin. J Biol Chem 2009 Sep;284(38): 25522-25531.

[2] Mikkel Christensen Dalsgaard, Mikkel Girke Jørgensen and Kenn Gerdes. Three new RelE-homologous mRNA interferases of Escherichia coli differentially induced by environmental stresses. Mol Microbiol 2010 Jan;75(2): 333-348.

[3] Larissa A. Singletary, Janet L. Gibson, Elizabeth J. Tanner, Gregory J. McKenzie, Peter L. Lee, Caleb Gonzalez, and Susan M. Rosenberg. An SOS-Regulated Type 2 Toxin-Antitoxin System. J Bacteriol 2009 Dec;191(24): 7456-7465.

Jump to AHL reporter assay page.

Jump to Home.