Difference between revisions of "Team:Tokyo Tech/AmiE Assay"
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<div id="contents_menu"> | <div id="contents_menu"> | ||
<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 | + | <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="link"><a href="#results">3. Results</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 | + | <h3 class="link"><a href="#methods">5. Materials and methods</a></h3> |
<h3 class="link"><a href="#construction"><font size="2.7"> 5-1. Construction</font></a></h3> | <h3 class="link"><a href="#construction"><font size="2.7"> 5-1. Construction</font></a></h3> | ||
| − | <h3 class="link"><a href="#protocol"><font size="2.7"> 5-2. Assay | + | <h3 class="link"><a href="#protocol"><font size="2.7"> 5-2. Assay protocol</font></a></h3> |
<h3 class="link"><a href="#reference">6. Reference</a></h3> | <h3 class="link"><a href="#reference">6. Reference</a></h3> | ||
</div><!-- /contents_menu --> | </div><!-- /contents_menu --> | ||
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<div id="summary" class="container"> | <div id="summary" class="container"> | ||
<div id="id_header" class="container_header"> | <div id="id_header" class="container_header"> | ||
| − | <h2><span>2. Summary of the | + | <h2><span>2. Summary of the experiment</span></h2> |
</div><!-- /_header --> | </div><!-- /_header --> | ||
<div id="summary_contents" class="container_contents"> | <div id="summary_contents" class="container_contents"> | ||
<p class="normal_text">The objective of this experiment is to characterize the function of AmiE protein. We prepared three samples shown below. When the AmiE degradation ability with these samples was analyzed, the results showed that C4HSL was not degraded by AmiE, but 3OC12HSL was degraded by AmiE.<br><br> | <p class="normal_text">The objective of this experiment is to characterize the function of AmiE protein. We prepared three samples shown below. When the AmiE degradation ability with these samples was analyzed, the results showed that C4HSL was not degraded by AmiE, but 3OC12HSL was degraded by AmiE.<br><br> | ||
| − | <p class="normal_text">A. PBAD/araC | + | <p class="normal_text">A. PBAD/araC ‐ <span style="font-style : italic">rbs ‐ amiE</span> (<a href="http://parts.igem.org/Part:BBa_K1949052">K1949052</a>) (pSB6A1)</p><br> |
<div align="center"><img src="https://static.igem.org/mediawiki/2016/b/b0/Fig.3-3-1-2-1.png" height="150"> <br></div> | <div align="center"><img src="https://static.igem.org/mediawiki/2016/b/b0/Fig.3-3-1-2-1.png" height="150"> <br></div> | ||
| − | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-3-1-2-1 </span>PBAD | + | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-3-1-2-1 </span>PBAD ‐ <i>rbs ‐ amiE</i> (pSB6A1) |
</p></div> | </p></div> | ||
| − | <p class="normal_text">B. Ptet | + | <p class="normal_text">B. Ptet ‐ <span style="font-style : italic">rbs ‐ luxR</span> ‐ <i>tt</i> ‐ Plux ‐ <span style="font-style : italic">rbs ‐ gfp</span> (pSB6A1)<br> |
<div align="center"><img src="https://static.igem.org/mediawiki/2016/b/b3/Fig.3-3-1-2-2.png" height="150"><br></div> | <div align="center"><img src="https://static.igem.org/mediawiki/2016/b/b3/Fig.3-3-1-2-2.png" height="150"><br></div> | ||
| − | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-3-1-2-2 </span>Pcon | + | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-3-1-2-2 </span>Pcon ‐ <i>rbs ‐ rhlR ‐ tt</i> ‐ Prhl ‐ <i>rbs ‐ gfp</i> (pSB6A1) |
</p></div> | </p></div> | ||
| − | <p class="normal_text">C. Ptet - <span style="font-style : italic">rbs | + | <p class="normal_text">C. Ptet - <span style="font-style : italic">rbs ‐ luxR</span> ‐ <i>tt</i> ‐ Plux ‐ <span style="font-style : italic">rbs ‐ gfp</span> (pSB6A1) |
<div align="center"><img src="https://static.igem.org/mediawiki/2016/a/a8/Fig.3-3-1-2-3.png" height="150"><br></div> | <div align="center"><img src="https://static.igem.org/mediawiki/2016/a/a8/Fig.3-3-1-2-3.png" height="150"><br></div> | ||
| − | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-3-1-2-3 </span>Pcon | + | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-3-1-2-3 </span>Pcon ‐ <i>rbs ‐ rhlR ‐ tt</i> ‐ Prhl ‐ <i>rbs ‐ gfp</i> (pSB6A1) |
</p></div> | </p></div> | ||
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<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 | + | <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"> | ||
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All the samples were XL1‐Blue strain.<br><br> | All the samples were XL1‐Blue strain.<br><br> | ||
<p class="normal_text">-Plasmids<br> | <p class="normal_text">-Plasmids<br> | ||
| − | A， PBAD/araC | + | A， PBAD/araC ‐ <span style="font-style : italic">rbs</span> ‐ <span style="font-style : italic">amiE</span> (pSB6A1)<br> |
| − | B， Ptet | + | B， Ptet ‐ <span style="font-style : italic">rbs ‐ luxR</span> ‐ <i>tt</i> ‐ Plux ‐ <span style="font-style : italic">rbs ‐ gfp</span> (pSB6A1)<br> |
| − | C， Ptet | + | C， Ptet ‐ <span style="font-style : italic">rbs ‐ rhlR</span> ‐ <i>tt</i> ‐ Prhl ‐ <span style="font-style : italic">rbs ‐ gfp</span> (pSB6A1) |
</p><br> | </p><br> | ||
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<div id="protocol"> | <div id="protocol"> | ||
<div id="protocol_header"> | <div id="protocol_header"> | ||
| − | <h3><span>5-2. Assay | + | <h3><span>5-2. Assay protocol</span></h3> |
</div><!-- /_header --> | </div><!-- /_header --> | ||
<div id="methods_contents"> | <div id="methods_contents"> | ||
| − | <p class="normal_text">1) Fresh | + | <p class="normal_text">1) Fresh culture<br> |
4 test tubes</p><br> | 4 test tubes</p><br> | ||
<div align="center"><img src="https://static.igem.org/mediawiki/2016/f/f5/Fig.3-3-1-5-1.jpg" height="300"><br></div> | <div align="center"><img src="https://static.igem.org/mediawiki/2016/f/f5/Fig.3-3-1-5-1.jpg" height="300"><br></div> | ||
<div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-3-1-5-1 </span> | <div align="center"><p class="caption" style="font-size: 16px; text-align: center;"><span style="font-weight: bold;">Fig. 3-3-1-5-1 </span> | ||
</p></div> | </p></div> | ||
| − | <p class="normal_text">2) Fresh | + | <p class="normal_text">2) Fresh culture<br> |
8 of 1.5 mL tubes</p><br> | 8 of 1.5 mL tubes</p><br> | ||
<div align="center"><img src="https://static.igem.org/mediawiki/2016/9/92/Fig.3-3-1-5-2.jpg" height="200"><br></div> | <div align="center"><img src="https://static.igem.org/mediawiki/2016/9/92/Fig.3-3-1-5-2.jpg" height="200"><br></div> | ||
Revision as of 12:17, 19 October 2016
3-3 AmiE assay
Contents
1. Introduction
The Prince coli expresses AmiE protein, and Snow White coli recovers from its apparent death and opens her eyes.
We tested the function of AmiE protein that influences the end of the story.
2. Summary of the experiment
The objective of this experiment is to characterize the function of AmiE protein. We prepared three samples shown below. When the AmiE degradation ability with these samples was analyzed, the results showed that C4HSL was not degraded by AmiE, but 3OC12HSL was degraded by AmiE.
A. PBAD/araC ‐ rbs ‐ amiE (K1949052) (pSB6A1)
Fig. 3-3-1-2-1 PBAD ‐ rbs ‐ amiE (pSB6A1)
B. Ptet ‐ rbs ‐ luxR ‐ tt ‐ Plux ‐ rbs ‐ gfp (pSB6A1)
Fig. 3-3-1-2-2 Pcon ‐ rbs ‐ rhlR ‐ tt ‐ Prhl ‐ rbs ‐ gfp (pSB6A1)
C. Ptet - rbs ‐ luxR ‐ tt ‐ Plux ‐ rbs ‐ gfp (pSB6A1)
Fig. 3-3-1-2-3 Pcon ‐ rbs ‐ rhlR ‐ tt ‐ Prhl ‐ rbs ‐ gfp (pSB6A1)
3. Results
We examined the AmiE degradation activity of C4 and C12. The results are shown below.
Fig. 3-3-1-3-1 AmiE degrades C12
Fig. 3-3-1-3-2 AmiE barely degrades C4
Several hours after adding AHL into E. coli solutions that induce and do not induce the AmiE expression respectively; we centrifugated this solutions and meassured the RFU of GFP / Turbidity of each supernatant. The results are showed in the graph above.
First lets look at the results of the AmiE degradation of C4; the RFU of GFP / Turbidity of the reporter added with the supernatant of the solution that induces the AmiE expression is almost the same as the one added with the supernatant of the solution that does not induce the AmiE expression
However, in the case of the degradation of C12, the RFU of GFP / Turbidity of the reporter added with the supernatant of the solution that induces the AmiE expression is about 1/10 of the one added with the supernatant of the solution that does not induce the AmiE expression. Based on the results above, we concluded that AmiE does not degrade C4 but degrades C12
4. Discussion
AmiE is the protein that degrades AHLs that have acyl chains longer than six carbons. This experiment showed that C4 was not degraded and C12 was degraded. This result is consistent with the AmiE function written in the literature.
We thought that we could express AmiE in the Prince coli and cause degradation of C12 as we desired. Also, it is expected that the Prince coli degrades the poisoned apple and makes Snow White coli recover from its apparent death.
5. Materials and methods
5-1. Construction
-Strain
All the samples were XL1‐Blue strain.
-Plasmids
A， PBAD/araC ‐ rbs ‐ amiE (pSB6A1)
B， Ptet ‐ rbs ‐ luxR ‐ tt ‐ Plux ‐ rbs ‐ gfp (pSB6A1)
C， Ptet ‐ rbs ‐ rhlR ‐ tt ‐ Prhl ‐ rbs ‐ gfp (pSB6A1)
5-2. Assay protocol
1) Fresh culture
4 test tubes
Fig. 3-3-1-5-1
2) Fresh culture
8 of 1.5 mL tubes
Fig. 3-3-1-5-2
control
Fig. 3-3-1-5-3
1. Inoculate A in 3 mL LB medium containing ampicillin (50 microg / mL), and add glucose so that the final concentration becomes 0.2%.
Inoculate B and C in 3 mL LB culture containing ampicillin (50 microg / mL).
2. Incubate all the samples at 37°C, 180 rpm for 12 h.
3. Dilute the overnight culture of A so that the turbidity becomes about 0.05.
4. Incubate at 37°C, 180 rpm so that turbidity becomes 0.16 to 0.18.
5. Add arabinose into test tube (ⅰ) and (ⅱ) so that the final concentration becomes 0.2%.
6. 2 h after adding arabinose, add 60 microL of 3OC12HSL (500 microM) into test tube (ⅰ) and (ⅲ), add 200 microL of 3OC12HSL (500 microM) into test tube (ⅱ) and (ⅳ).
7. 5 h after adding AHLs, dispense the fresh cultures into 1.5 mL tubes, and centrifuge in duplicate for 2 min at 18000G.
8. Transfer supernatant to another 1.5 mL tube.
9. Add each 10 microL overnight culture for B and C into 800 microL LB medium containing ampicillin (50 microg / mL). Also, add each 10 microL overnight culture for B and C into 1 mL LB medium containing ampicillin (50 microg / mL) for controls. (B: a, c, e, g) (C: b, d, f, h)
10. After 1.5 h, add 200 microL supernatants of A into (ⅰ), (ⅱ), (ⅲ) and (ⅳ), and add 4 of microL 3OC12HSL into tube (e), 13.3 of microL C4HSL into tube (f), 4 of microL DMSO into tube (g), 13.3 microL of DMSO into tube (h) for controls.
11. Incubate at 37°C, 180 rpm for 4 h.
12. Measure RFU of GFP and the Turbidity.
6. Reference
[1]Ochiai S, Yasumoto S, Morohoshi T, Ikeda T. AmiE, a Novel N-Acylhomoserine
Lactone Acylase Belonging to the Amidase Family, from the Activated-Sludge Isolate Acinetobacter sp. Strain Ooi24. 2014 Nov;80(22):6919-25.
