Difference between revisions of "Team:Tokyo Tech/Toxin Assay/mazEF System Assay"

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<p class="normal_text">We constructed the plasmid mazF placed downstream of Pbad, the mazE downstream of Pcon, so that Arabinose can induce MazF (toxin) expression. Additionally, we tried clarifying stoichiometric proportion by changing the expression level of MazE with two types of RBS (B0034 and J61117) downstream of Pcon. We used <span style="font-style : italic">E. coli</span> transformed as follows in the experiment.
+
<p class="normal_text">We constructed the plasmid <span style="font-style : italic">mazF</span> placed downstream of PBAD, the <span style="font-style : italic">mazE</span> downstream of Pcon, so that arabinose can induce MazF (toxin) expression. Additionally, we tried clarifying stoichiometric proportion by changing the expression of MazE with two types of RBS (B0034 and J61117) downstream of Pcon. We used <span style="font-style : italic">E. coli</span> transformed as follows in the experiment.
 
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<p class="normal_text"><span style="font-style : italic">E. coli</span> encoded MazE downstream of weak RBS (J61117) reached stationary phase with smaller turbidity and RFU of GFP than that of normal RBS (B0034). <span style="font-style : italic">E. coli</span> encoded mazE downstream of normal RBS (B0034) reached almost the same stationary phase as <span style="font-style : italic">E. coli</span> without TA system.</p><br>
+
<p class="normal_text"><span style="font-style : italic">E. coli</span> encoded MazE downstream of weak RBS (J61117) reached stationary phase with smaller turbidity and RFU of GFP than that of normal RBS (B0034). <span style="font-style : italic">E. coli</span> encoded <span style="font-style : italic">mazE</span> downstream of normal RBS (B0034) reached almost the same stationary phase as <span style="font-style : italic">E. coli</span> without TA system.</p><br>
  
 
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<p class="normal_text">We constructed the plasmid mazF placed downstream of Pbad, the mazE downstream of Pcon, so that Arabinose can induce MazF (toxin) expression. Additionally, we tried clarifying stoichiometric proportion by changing the expression level of MazE with two types of RBS (B0034 and J61117) downstream of Pcon. We used <span style="font-style : italic">E. coli</span> transformed as follows in the experiment.
+
<p class="normal_text">We constructed the plasmid <span style="font-style : italic">mazF</span> placed downstream of PBAD, the <span style="font-style : italic">mazE</span> downstream of Pcon, so that Arabinose can induce MazF (toxin) expression. Additionally, we tried clarifying stoichiometric proportion by changing the expression level of MazE with two types of RBS (B0034 and J61117) downstream of Pcon. We used <span style="font-style : italic">E. coli</span> transformed as follows in the experiment.
 
</p><br>
 
</p><br>
 
<div align="center"><img src="https://static.igem.org/mediawiki/2016/e/e7/T--Tokyo_Tech--3-1-2-2-2-1.png" height="150"><br></div>
 
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<div id="2.results_contents" class="container_contents">
<p class="normal_text"><span style="font-style : italic">E. coli</span> encoded MazE downstream of weak RBS (J61117) reached stationary phase with smaller turbidity and RFU of GFP than that of normal RBS (B0034). <span style="font-style : italic">E. coli</span> encoded mazE downstream of normal RBS (B0034) reached almost the same stationary phase as <span style="font-style : italic">E. coli</span> without TA system.</p>
+
<p class="normal_text"><span style="font-style : italic">E. coli</span> encoded <span style="font-style : italic">mazE</span> downstream of weak RBS (J61117) reached stationary phase with smaller turbidity and RFU of GFP than that of normal RBS (B0034). <span style="font-style : italic">E. coli</span> encoded <span style="font-style : italic">mazE</span> downstream of normal RBS (B0034) reached almost the same stationary phase as <span style="font-style : italic">E. coli</span> without TA system.</p>
  
 
<div align="center"><img src="https://static.igem.org/mediawiki/2016/2/26/T--Tokyo_Tech--Description_Toxin6.png" width="400px"/>
 
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<p class="normal_text">From this experimental result, we found that MazF inhibits cell growth and translation with MazE. Additionally, Fig 3.1.2.2.8 showed that more expression level of MazE, less likely inhibited translation of MazF stoichiometrically.<br>
 
<p class="normal_text">From this experimental result, we found that MazF inhibits cell growth and translation with MazE. Additionally, Fig 3.1.2.2.8 showed that more expression level of MazE, less likely inhibited translation of MazF stoichiometrically.<br>
 
Therefore the result suggests that MazF inhibits translation, and <span style="font-style : italic">mazE</span> resuscitates the translation inhibition; resuscitation correlates MazE expression level. This experimental result is associated with anamnestic experimental results indicated that MazE and MazF form a hexamer (MazF2-MazE2-MazF2)<br>
 
Therefore the result suggests that MazF inhibits translation, and <span style="font-style : italic">mazE</span> resuscitates the translation inhibition; resuscitation correlates MazE expression level. This experimental result is associated with anamnestic experimental results indicated that MazE and MazF form a hexamer (MazF2-MazE2-MazF2)<br>
The results of Experiment 1.2.1. and Experiment 1.2.2. seem that using <span style="font-style : italic">mazEF</span> System can repeat the inhibition of cell growth and translation by a toxin, and resuscitation of cell growth and translation by an antitoxin.  
+
The results of Experiment 1.2.1. and Experiment 1.2.2. seem that using <span style="font-style : italic">mazEF</span> System can repeat the inhibition of cell growth and translation by the toxin, and resuscitation of cell growth and translation by the antitoxin.  
  
 
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                     -plasmid<br>
 
                     -plasmid<br>
1) Pbad _<span style="font-style : italic">rbs</span>(pSB6A1) + Plac_<span style="font-style : italic">rbs</span> (pSB3K3)<br>
+
1) PBAD-<span style="font-style : italic">rbs</span> (pSB6A1) + Plac-<span style="font-style : italic">rbs</span> (pSB3K3)<br>
2) Pcon_<span style="font-style : italic">rbs_gfp</span> (pSB6A1) + Plac_<span style="font-style : italic">rbs</span>(pSB3K3)<br>
+
2) Pcon-<span style="font-style : italic">rbs-gfp</span> (pSB6A1) + Plac-<span style="font-style : italic">rbs</span> (pSB3K3)<br>
3) Pbad_<span style="font-style : italic">rbs_mazF</span>_TT_Pcon_<span style="font-style : italic">rbs_gfp</span> (pSB6A1) + Pcon_<span style="font-style : italic">rbs(weak)_mazE</span> (pSB3K3)<br>
+
3) PBAD-<span style="font-style : italic">rbs-mazF-tt</span>-Pcon-<span style="font-style : italic">rbs-gfp</span> (pSB6A1) + Pcon-<span style="font-style : italic">rbs</span>(weak)-mazE (pSB3K3)<br>
4) Pbad_<span style="font-style : italic">rbs_mazF</span>_TT_Pcon_<span style="font-style : italic">rbs_gfp</span> (pSB6A1) + Pcon_<span style="font-style : italic">rbs_mazE</span> (pSB3K3)<br>
+
4) PBAD-<span style="font-style : italic">rbs-mazF-tt</span>-Pcon-<span style="font-style : italic">rbs-gfp</span> (pSB6A1) + Pcon-<span style="font-style : italic">rbs-mazE</span> (pSB3K3)<br>
5) Pbad_<span style="font-style : italic">rbs_mazF</span>_TT_Pcon_<span style="font-style : italic">rbs_gfp</span> (pSB6A1) + vector only (pSB3K3)
+
5) PBAD-<span style="font-style : italic">rbs-mazF-tt</span>-Pcon-<span style="font-style : italic">rbs-gfp</span> (pSB6A1) + vector only (pSB3K3)
  
 
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<p class="normal_text">Pre-culture<br>
 
<p class="normal_text">Pre-culture<br>
1. Suspend colonies on a master plate into LB medium containing ampicillin (50 macrog / mL) and kanamycin (50 macrog / mL).<br>
+
1. Suspend colonies on a master plate into LB medium containing ampicillin (50 microg / mL) and kanamycin (50 microg / mL).<br>
 
2. Incubate with vigorous shaking for 12 h.<br><br>
 
2. Incubate with vigorous shaking for 12 h.<br><br>
  

Revision as of 06:21, 16 October 2016

3-1-2-1 Stop & Go

1-1. Introduction

In Experiment 1-2-1., we found that a toxin inhibits cell growth, and an antitoxin resuscitates it. However, what happens when a toxin is expressed after the antitoxin constitutive expression? Therefore, we conducted the experiment. Since cell growth was resuscitated after cells had grown, we named this experiment, "Go & Stop".

1-2. Summary of the Experiment

We constructed the plasmid mazF placed downstream of PBAD, the mazE downstream of Pcon, so that arabinose can induce MazF (toxin) expression. Additionally, we tried clarifying stoichiometric proportion by changing the expression of MazE with two types of RBS (B0034 and J61117) downstream of Pcon. We used E. coli transformed as follows in the experiment.



Fig. 3-1-2-2-2-1.



Fig. 3-1-2-2-2-2.



Fig. 3-1-2-2-2-3.



Fig. 3-1-2-2-2-4.



Fig. 3-1-2-2-2-5.

1-3. Results

E. coli encoded MazE downstream of weak RBS (J61117) reached stationary phase with smaller turbidity and RFU of GFP than that of normal RBS (B0034). E. coli encoded mazE downstream of normal RBS (B0034) reached almost the same stationary phase as E. coli without TA system.


Fig. 3-1-2-2-3-1.


Fig. 3-1-2-2-3-2


4. Discussion

The expression level of Prhl was so weak and the leak was high that Queen-like coli could not influence to Snow White-like coli, in other words, our final genetic circuits could not work. Taken together the results below, we re-recognated that we have to improve Prhl strength to work our final circuits.

5. Materials and Methods

5-1. Construction

-Strain All the plasmids were prepared in XL1-Blue strain.
-Plasmids A. Pcon-rhlR-ssrA(pSB6A1), Prhl-rbs-lasI-rbs-gfp-ssrA (pSB3K3) (Fig. 3-2-2-5-1)



Fig. 3-2-2-5-1 Pcon-rhlR-ssrA(pSB6A1), Prhl-rbs-lasI-rbs-gfp-ssrA (pSB3K3)

B. Pcon-luxI(pSB6A1), Plux-rbs-rhlI-rbs-rfp-ssrA (pSB3K3) (Fig. 3-2-2-5-2)



Fig. 3-2-2-5-2 Pcon-luxI(pSB6A1), Plux-rbs-rhlI-rbs-rfp-ssrA (pSB3K3)

C. pSB6A1, pSB3K3…Negative (Fig. 3-2-2-5-3)



Fig. 3-2-2-5-3 pSB6A1, pSB3K3

-Medium
LB medium AK
LB medium containing ampicillin (50 microg/ mL) and kanamycin (50 microg/ mL)





5-2. Assay Protocol

The following experiments is performed at 37℃ unless otherwise stated.

1) Prepare the overnight cultures in LB medium AK at 180 rpm.

2) Dilute the overnight cultures to 1/60 in fresh LB medium AK at 700 rpm for 1 h.

3) Add C4 (100 microM) into Queen-like coli and C12 into Snow White-like coli, and incubate them at 700 rpm for 4 h.

4) Measure RFU of GFP / Turbidity of GFP at 490nm as an exciting wavelength, 525nm as a measurement wavelength.

6. Reference

(1) Bo Hu et al. (2010) An Environment-Sensitive Synthetic Microbial Ecosystem. PLoS ONE 5(5): e10619
(2) Chen M. Zhang et al (2014) Distributed implementation of the genetic double-branch structure in Escherichia coli. Chinese Science Bulletin 59: 4625-4630

3-1-2-1 Go & Stop

2-1. Introduction

In Experiment 1-2-1., we found that a toxin inhibits cell growth, and an antitoxin resuscitates it. However, what happens when a toxin is expressed after the antitoxin constitutive expression? Therefore, we conducted the experiment. Since cell growth was resuscitated after cells had grown, we named this experiment, "Go & Stop".

2-2. Summary of the Experiment

We constructed the plasmid mazF placed downstream of PBAD, the mazE downstream of Pcon, so that Arabinose can induce MazF (toxin) expression. Additionally, we tried clarifying stoichiometric proportion by changing the expression level of MazE with two types of RBS (B0034 and J61117) downstream of Pcon. We used E. coli transformed as follows in the experiment.



Fig. 3-1-2-2-2-1.



Fig. 3-1-2-2-2-2.



Fig. 3-1-2-2-2-3.



Fig. 3-1-2-2-2-4.



Fig. 3-1-2-2-2-5.

2-3. Results

E. coli encoded mazE downstream of weak RBS (J61117) reached stationary phase with smaller turbidity and RFU of GFP than that of normal RBS (B0034). E. coli encoded mazE downstream of normal RBS (B0034) reached almost the same stationary phase as E. coli without TA system.

Fig. 3-1-2-2-3-1.


Fig. 3-1-2-2-3-2


Fig. 3-1-2-2-3-3


Fig. 3-1-2-2-3-4


2-4. Discussion

From this experimental result, we found that MazF inhibits cell growth and translation with MazE. Additionally, Fig 3.1.2.2.8 showed that more expression level of MazE, less likely inhibited translation of MazF stoichiometrically.
Therefore the result suggests that MazF inhibits translation, and mazE resuscitates the translation inhibition; resuscitation correlates MazE expression level. This experimental result is associated with anamnestic experimental results indicated that MazE and MazF form a hexamer (MazF2-MazE2-MazF2)
The results of Experiment 1.2.1. and Experiment 1.2.2. seem that using mazEF System can repeat the inhibition of cell growth and translation by the toxin, and resuscitation of cell growth and translation by the antitoxin.

2-5. Materials and Methods

2-5-1. Construction

-Strain
All the samples were XL1-Blue strain.

-plasmid
1) PBAD-rbs (pSB6A1) + Plac-rbs (pSB3K3)
2) Pcon-rbs-gfp (pSB6A1) + Plac-rbs (pSB3K3)
3) PBAD-rbs-mazF-tt-Pcon-rbs-gfp (pSB6A1) + Pcon-rbs(weak)-mazE (pSB3K3)
4) PBAD-rbs-mazF-tt-Pcon-rbs-gfp (pSB6A1) + Pcon-rbs-mazE (pSB3K3)
5) PBAD-rbs-mazF-tt-Pcon-rbs-gfp (pSB6A1) + vector only (pSB3K3)





2-5-2. Assay Protocol

Pre-culture
1. Suspend colonies on a master plate into LB medium containing ampicillin (50 microg / mL) and kanamycin (50 microg / mL).
2. Incubate with vigorous shaking for 12 h.

Incubation and Assay
1. Measure the turbidity of the pre-cultures.
2. Dilute the pre- cultures to 1 / 30 into LB medium containing 4 mL ampicillin and kanamycin.
3. Incubate with vigorous shaking so that turbidity becomes 0.03
4. Add arabinose so that the final concentration becomes 0.02%.
5. Incubate with vigorous shaking for 24 h, and measure turbidity and RFU of GFP at proper times.