We conducted an experiment and simulated to confirm that the above four scenes can be represented. We introduced concepts in each scene and demonstrated them. Additionally, based on them, we simulated the representation of Snow White story.
5.1 Cold inducible promoter functions at 18°C in Scene 1
It is a cold inducible promoter (called Pcold commonly) that plays a most important role in this Scene. This story never begins unless the Magic Mirror answers the Queen’s question.
The experiment was conducted with BBa_1949001. We cultivated for each sample at 18°C and 37°C and measured the GFP / Turbidity with a plate reader. The experimental result showed that samples cultured at 18°C had higher fluorescence intensity of GFP than those cultured at 37°C.
Thus, we found that the story begins by lowering the culture temperature.
5.2 The screening of rhl promoter with optimal strength for Scene 2
The Queen coli gave the Poisoned Apple, and Snow White coli falls asleep. We use cell-cell communication to represent this scene, so we need the reporter with optimal strength to make the genetic circuit designed by us work properly.
Therefore, we introduce rhl system assay as a concept in this Scene. We improved the function of rhl promoter through the process listed below and succeeded in newly obtaining of optimal rhl promoter mutants for our project.
5.2.2 rhlプロモーターの強度に関するシミュレーション
First of all, we evaluated the activities the existing promoters: Prhl(BBa_I14017), Plux(BBa_R0062), Plas(BBa_R0079) when added 3 types of AHLs.
The above diagram shows the intensity of the two promoters should be in the red region in the figure. The green point shows the relationships of the promoters which we intended to use primarily. In order to move to the red region, we found that it is needed to improve Prhl and increase its expression level.
5.2.3 Improvement of Prhl
We made mutants of rhl promoter by inserting a point mutation into the wild type (WT) rhl promoter.
In the experiment, we added reagent AHLs into the reporters and examined their fluorescence intensities.
As a result, we succeeded in newly obtaining stronger mutants than the WT Prhl (NM).
iGEM Tokyo_Tech has Improved rhl promoter in the past. However, comparing the Prhl (NM) to Prhl (LR), the SN ratio of Prhl (NM) was higher than that of Prhl (LR). Futuremore, the result shows that Prhl (LR)has crosstalk with C12-AHL at a constant rate. When representing Snow White story, and the crosstalk to C12 happens, the Queen coli will suicide by eating the Poisoned Apple made by herself. Therefore, we made the mutants using WT as a template.
5.3 azF-MazE system as Toxin-Antitoxin system can be controlled in Scene 3
In this Scene, we introduce TA system as a concept.
If we do not show that translation is inhibited by MazF, and translation is restarted by MazE, we cannot represent the key part of the story that "Snow White falls down by the Poisoned Apple and wake up again by the Prince.”
In this experiment, we used the BBa_K1949100 and Bba_1949102.
First, MazF was expressed by arabinose, and 2 h later, the MazE was expressed by IPTG.
From the experimental results, we found that the turbidity of samples without MazE did not rise. However, we also found that E. coli restarts its cell growth when MazE is expressed by adding IPTG.
Moreover, when only MazF worksed, the RFU of GFP hardly rose, but when MazE was induced, the RFU of GFP rose. (link: toxin assay)
From the above, we found that MazF stops cell growth and translation of E. coli, but MazE restarts cell growth that have stopped and furthermore restarts translation.
According to the experiments, we showed that TA system works properly.
5.4 AmiE degrades 3OC12HSl selectively and does not degrade C4HSL in Scene 4
In the final Scene, we introduce the selective degradation of AHLs by AmiE as a concept.
As shown in the TA system, we found that Snow White can wake up again because MazE counteracts the function of MazF. However, we have not showed the trigger, that is, the degradation of only 3OC12HSL by the Prince coli. Therefore, we examined whether AmiE selectively degrades AHLs.
From the experimental results, when C12 was added to the culture skution of E. coli where AmiE was expressed, C12 was degraded, whereas C4 was hardly degraded.
For these reasons, we showed that AmiE selectively degrades AHLs, only C12 in this project.
5.5 the simulation related to the story
From the results of wet lab, it was showed that the designed circuit works properly at each point. We simulated the representation of the story in a combination of these Points.
5.5.1. When the Prince comes?
We simulated to confirm which is better, the Prince coli exist from the beginning, that is, the Prince has known Snow White and watches her grow or he comes across her, in order to make our genetic circuit work.
As a result, we found that when the Prince coli is added from the beginning, AmiE produced by the Prince coli increases and C12 is overdegraded. Then, C12 cannot exist in the medium (Fig. 2), and the circuit does not work correctly.
On the other hand, when the Prince coli is added at t = 700, the number of the Prince coli does not increase greatly (Fig3). Therefore, C12 can exist until t = 70, and after that C12 decreases with an increase in AmiE (Fig4).
From this result, it was found that the genetic circuit works well by adding the Prince coli at t=700. In other words, as with the original story, the Prince coli comes across Snow White coli at t=700 and rescues her.
5.5.2 representation of the story
As a result of simulation, we obtained and confirmed the desirable behavior of the whole system by modifying and improving parts. As described below, our simulation showed appropriate transition of fluorescence for the story.
Based on the simulation, we will show you which one is a real beauty, Snow White coli or the Queen coli.
In the blue area of Fig, the fluorescence intensity of Snow White coli exceeds the Queen coli’s.
That is because one day, Snow White coli’s beauty exceeded the Queen coli’s beauty. Snow White got fairer and fairer.
In the pink area of Fig, added C4 leads to production of C12. Because of this, MazF, a toxin, increases in the Queen coli, and suppresses increase of fluorescence protein. It looks as if after the Magic Mirror’s answer, the Queen transformed herself into a Witch and gave the Poisoned Apple to Snow White. This is the scene where the Queen is mad with jealousy and drifts into crime
In the green area of Fig, C12 increases, and MazF induced by C12 increases in Snow White coli, which causes GFP excess over RFP. It looks as if Snow White bit the apple, then sank into unconsciousness soon
In the yellow area of Fig, since AmiE produced by the added Prince coli degrades C12, MazF in Snow White coli decreases and increases C4. It looks as if the Prince lifted Snow White and she opened her eyes.
From the above, we were able to represent the story by the genetic circuit we designed, and furthermore, it was found that Snow White coli is a real beauty.
