Difference between revisions of "Part:BBa K4743030"

Revision as of 15:36, 9 October 2023

Bacillus subtilis Hydrogen sulfide based kill switch

Kill switch’s mechanism

In Figure 3, we depict the initial exposure to normal conditions. In this scenario, when hydrogen sulfide levels are low, the translated SqrR protein (red) effectively represses the sqr promoter, resulting in the prevention of transcription for recombinases DRE or CRE ( gray) and the antitoxin (pink). Furthermore, the presence of terminator sequences labeled by rox or Lox sequences puts a halt to the transcription of the toxin. Consequently, under these conditions, the absence of both toxin and antitoxin prevents any cell death.

Figure 3: First exposure to the normal condition

In the second condition, as illustrated in Figure 4 and 5, when the organism is exposed to the gut environment characterized by the presence of hydrogen sulfide (depicted as one yellow dot with two blue dots), the suppressive effect of the SqrR protein (red) decreases. This reduction in suppression leads to the transcription of recombinase DRE or CRE (gray) and the antitoxin. The recombinase, in turn, targets the terminator sequence labeled by rox/Lox and cleaves it, enabling the transcription of the toxin(blue). However, it's important to note that the transcribed antitoxin (pink) counteracts the toxin, neutralizing its toxic activity. In conclusion, under these conditions, the presence of both toxin and antitoxin allows the cell to remain viable.

Figure 4-5: exposure to the gut environment

In the third condition, depicted in Figure 6, we illustrate the organism's return to the normal environment, indicating its escape from the gut or excretion of feces. Under these circumstances, the SqrR suppressor (depicted in red) once again binds to the promoter, effectively inhibiting the transcription of the antitoxin. However, crucially, the terminator that normally halts toxin transcription is excised. This excision allows for the transcription of the toxin. In this scenario, the bacteria lose the protective antitoxin, leading to cell death as a consequence.

Figure 6: Second exposure to the normal environment

Bacillus subtilis We tailored our kill switch for Bacillus subtilis, selecting MazF as the toxin and MazE as the antitoxin, with DRE serving as our recombinase. Additionally, we carefully chose a promoter and terminator that are compatible with Bacillus subtilis, ensuring the effectiveness of our engineered system. This kill switch is shown at BBa_K4743030.

Figure 7: kill switch of Bacillus Subtilis

Figure 8: The map of Bacillus subtilis kill switch

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 464
Illegal AgeI site found at 1623
1000
INCOMPATIBLE WITH RFC[1000]
Illegal SapI.rc site found at 677

@@ Line 5: / Line 5: @@
 <span class='h3bb'><big>'''Kill switch’s mechanism'''</big></span>
-The graph below (Figure 1) shows the first exposure to the normal condition. When there is a low amount of hydrogen sulfide, the translated sqrR protein (red) represses the sqr promoter, preventing the transcription of recombinase DRE or CRE and the antitoxin . Additionally, the terminator labeled by rox sequences halts the transcription of toxin. Consequently, no death occurs because there is no toxin and antitoxin present.
+In Figure 3, we depict the initial exposure to normal conditions. In this scenario, when hydrogen sulfide levels are low, the translated SqrR protein (red) effectively represses the sqr promoter, resulting in the prevention of transcription for recombinases DRE or CRE ( gray) and the antitoxin (pink). Furthermore, the presence of terminator sequences labeled by rox or Lox sequences puts a halt to the transcription of the toxin. Consequently, under these conditions, the absence of both toxin and antitoxin prevents any cell death.
-<html><img style="width:800px" src="https://static.igem.wiki/teams/4743/wiki/folder-for-parts/kill-switch-first-exposure.png" </html>
+Figure 3: First exposure to the normal condition
-<center>Figure 1: First exposure to the normal condition. </center>
-The second condition is exposure to the gut environment(shown in figure 2). When the organism is exposed to the gut, which hydrogen sulfide(Blue) presents , the suppressive effect of the sqrR suppressor decreases, resulting in the transcription of recombinase DRE or CRE and the antitoxin .The recombinase DRE targets the terminator sequence labeled by rox and cleaves it, allowing the toxin to be transcribed. However, the transcribed antitoxin neutralizes the toxin and inhibits its toxic activity. In conclusion, the cell remains alive.
+In the second condition, as illustrated in Figure 4 and 5, when the organism is exposed to the gut environment characterized by the presence of hydrogen sulfide (depicted as one yellow dot with two blue dots), the suppressive effect of the SqrR protein (red) decreases. This reduction in suppression leads to the transcription of recombinase DRE or CRE (gray) and the antitoxin. The recombinase, in turn, targets the terminator sequence labeled by rox/Lox and cleaves it, enabling the transcription of the toxin(blue). However, it's important to note that the transcribed antitoxin (pink) counteracts the toxin, neutralizing its toxic activity. In conclusion, under these conditions, the presence of both toxin and antitoxin allows the cell to remain viable.
-<html><img style="width:800px" src="https://static.igem.wiki/teams/4743/wiki/folder-for-parts/kill-switch-in-gut-environment.png" </html>
-<center>Figure 2:  exposure to the gut environment. </center>
-The third condition(Figure 3)represents the organism's second exposure to the normal environment, which signifies its escape from the gut or excretion of feces. In this condition, the sqrR suppressor binds to the promoter once again, restricting transcription of antitoxin. However, the terminator that halts toxin transcription is excised, resulting in the transcription of the toxin. In this scenario, the bacteria lose the antitoxin, ultimately leading to cell death.
+Figure 4-5:  exposure to the gut environment
-<html><img style="width:800px" src="https://static.igem.wiki/teams/4743/wiki/folder-for-parts/kill-switch-second-exposure.png" </html>
+In the third condition, depicted in Figure 6, we illustrate the organism's return to the normal environment, indicating its escape from the gut or excretion of feces. Under these circumstances, the SqrR suppressor (depicted in red) once again binds to the promoter, effectively inhibiting the transcription of the antitoxin. However, crucially, the terminator that normally halts toxin transcription is excised. This excision allows for the transcription of the toxin. In this scenario, the bacteria lose the protective antitoxin, leading to cell death as a consequence.
-<center>Figure 3: Second exposure to the normal environment. </center>
+Figure 6: Second exposure to the normal environment
+Bacillus subtilis
+We tailored our kill switch for Bacillus subtilis, selecting MazF as the toxin and MazE as the antitoxin, with DRE serving as our recombinase. Additionally, we carefully chose a promoter and terminator that are compatible with Bacillus subtilis, ensuring the effectiveness of our engineered system. This kill switch is shown at BBa_K4743030.
+Figure 7: kill switch of Bacillus Subtilis
+Figure 8: The map of Bacillus subtilis kill switch