Difference between revisions of "Part:BBa K2970004"

Revision as of 02:03, 22 October 2019

Trigger 2 Composition

Trigger 2 forms together with Trigger 1 (BBa_K2970000) a complex due to complementary regions, as shown in Figure 1A. This complex can open a gate (BBa_K2970002, Figure 1B) to enable translation of a gene that is locked with this gate to regulate translation. After binding of the trigger complex due to complementarity, the hairpin of the gate will open and release the ribosome binding site and the start codon, thus translation can occur (Figure 2). The affinity between the trigger complex and the gate is greater than that of the gate to itself (in the loop). A single trigger cannot open the gate because it has only half the required complementary sequence.

**Figure 1:** A) Formation of trigger complex after translation. B) mRNA of gate sequence forms secondary structures that hide the ribosome binding site and the start codon.

**Figure 2:** Opening of the gate due to annealing of trigger complex to gate.

We used this system to regulate a chloramphenicol resistance, which is locked by the gate. To transform the trigger into bacteria it should be put on a plasmid together with a promoter and a terminator as we did with this part. After transformation of both trigger plasmids (BBa_K2970003 and BBa_K2970004) and the gate plasmid (BBa_K2970006) in one bacterium all three mRNA structures will be formed, the gate will be opened, and the translation of the chloramphenicol resistance can take place. Bacteria that took all three plasmids are able to survive on media with chloramphenicol. This system can be used to transform many genes of interest on three different plasmids into bacteria with only using one antibiotic resistance instead of three different resistances.

Usage and Biology

This part can be used together with the other trigger composition and the gate composition for triple transformation in bacteria. Genes of interest that should be transformed together, can be put on the three plasmids. Only if all three plasmids are taken by a bacterium the chloramphenicol resistance is produced and the bacterium can survive on medium with chloramphenicol. Thus chloramphenicol can be used to select for bacteria that got all genes of interest.

Results

We tested the gate plasmid with our two trigger plasmids by performing simultaneous transformations with these plasmids. After transformation we selected the bacteria by plating on LB-agar plates with chloramphenicol. We compared the results with positive and negative controls, using the empty pSB1C3 backbone and pSB1A3 respectively. The result of the transformation with all three plasmids after selection with chloramphenicol is shown in Figure 3.

**Figure 3:** A) *E. coli* cells transformed with three plasmids, the plasmid carrying the gate, the plasmid carrying trigger one and the plasmid carrying trigger two. The cells were plated on LB-agar plates with chloramphenicol, bacterial growth was observed.

Colonies grew on chloramphenicol plates after transformation with all three plasmids. This shows that our RNA based logic circuit allows the expression of the antibiotic resistance. No colonies grew on the plates with the negative control. Colonies also grew on the plates with the positive control. To further test the trigger and the gate, we performed transformations with each plasmid individually. The results are shown in Figure 4.

**Figure 4:** A) Cell plated out on chloramphenicol agar plates. Left: cells transformed with the gate plasmid. Middle: cells transformed with the trigger 1 plasmid. Right: cells transformed with the trigger 2 plasmid.

Unfortunately colonies also grew on the plates with just the individual transformation of the gate plasmid, though the number of colonies was much lower when compared to the transformation with all three plasmids. We sequenced the gate plasmid to confirm correct assembly. The results showed no mutation in the gate sequence. We concluded that the gate is showing signs of leakage, expressing the antibiotic resistance even in the absence of triggers. This basal expression was rather strong due to the strong promoter we used for our experiments. To measure the gates leakage, we observed cells transformed with all three plasmids on plates with different chloramphenicol concentrations and compared them to cells transformed with only the gate plasmid. As a positive control we used the pSB1C3 backbone. The number of colonies per plate after twelve hours of incubation is shown in Figure 5.

**Figure 5:** A) Number of colonies per plate depending on the chloramphenicol concentration. *E. coli* DH5α cells were transformed with the gate plasmid (blue), the gate plasmid together with both trigger plasmids (red), or with the control backbone pSB1C3 (green). The colonies were counted after 12 hours.

The data clearly shows that the gate is leaking, but when compared to the triple transformation (red) and the control (green) the number of colonies when transformed with only the gate plasmid was significantly lower. Additionally the number of colonies when transformed with all three plasmids was larger than when transformed with the positive control.

We also used a plate reader to measure the growth rate of cells that were transformed with three different plasmids (pSB1A3, pSB1C3, pSB1K3 or BBa_K2970003, BBa_K2970004, BBa_K2970006) and compared it to cells without any plasmids. The results are shown in Figure 6.

**Figure 6:** A) Plate reader growth curves of E. coli DH5α. The generation time was measured and calculated for non competent cells (orange), for cells transformed with the backbones pSB1A3, pSB1C3 and pSC1K3.M1 (blue), and for cells transformed with our two trigger plasmids together with the gate plasmid (green). Error bars show the standard deviation.

For cells transformed with three plasmids an impaired growth rate can be observed. We could not show that the transformation of our three plasmids was less harmful to the bacteria than the transformation with three different antibiotics, instead it shows comparable levels of stress.

Due to the linker between the gate and our gene of interest (chloramphenicol acetyl transferase) additional bases were attached to the gene which might affect the functionality of the protein as it contained an additional 19 amino acids. To test the genes activity we inserted the sequence containing the additional bases into pSB1A3, transformed it into bacteria and plated the cells on chloramphenicol plates. The results of this experiment are shown in Figure 7.

**Figure 7:** Test transformation to check chloramphenicol resistance gene. E. coli DH5α cells were transformed with a test plasmid containing the modified chloramphenicol resistance gene (A). For negative control (B) pSB1A3 was used. For positive control (C) pSB1C3 was used.

Several colonies grew on the plate with bacteria transformed with the modified chloramphenicol acetyl transferase. The negative control showed no cell growth while on the plate with the positive control a cell turf has grown. This confirms that the activity of the chloramphenicol acetyl transferase was not significantly impaired by the additional amino acids.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 7
Illegal NheI site found at 30
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

@@ Line 28: / Line 28: @@
 ===Results===
-We tested this part by performing triple transformations of this part in pSB1A3 together with the other trigger composition and the gate composition, in pSB1A3 backbones as well. After transformation we selected by plating the bacteria on plates with chloramphenicol. We compared the results with positive and negative controls. Furthermore we did single transformation of each part.
+We tested the gate plasmid with our two trigger plasmids by performing simultaneous transformations with these plasmids. After transformation we selected the bacteria by plating on LB-agar plates with chloramphenicol. We compared the results with positive and negative controls, using the empty <partinfo>pSB1C3</partinfo> backbone and <partinfo>pSB1A3</partinfo> respectively.
-We had colonies on plates with bacteria transformed with both trigger plasmids and the gate plasmid, showed in Figure 1.
+The result of the transformation with all three plasmids after selection with chloramphenicol is shown in Figure 3.
 <html>
 <figure>
-<img  width="70%" src="https://2019.igem.org/wiki/images/4/48/T--Hamburg--ResultsFigure5.jpeg">
+<img width="50%" src="https://2019.igem.org/wiki/images/4/48/T--Hamburg--ResultsFigure5.jpeg">
 <figcaption>
-<b>Figure 1: </b>Cells, transformed with three plasmids (containing trigger 1 composition, trigger 2 composition, and gate composition) plated out on chloramphenicol agar plates.
+<b>Figure 3: </b>A) <i>E. coli</i> cells transformed with three plasmids, the plasmid carrying the gate, the plasmid carrying trigger one and the plasmid carrying trigger two. The cells were plated on LB-agar plates with chloramphenicol, bacterial growth was observed.
 </figcaption>
 </figure>
 </html>
+Colonies grew on chloramphenicol plates after transformation with all three plasmids. This shows that our RNA based logic circuit allows the expression of the antibiotic resistance. No colonies grew on the plates with the negative control. Colonies also grew on the plates with the positive control.
+To further test the trigger and the gate, we performed transformations with each plasmid individually. The results are shown in Figure 4.
 <html>
 <figure>
-<img  width="100%" src="https://2019.igem.org/wiki/images/e/ec/T--Hamburg--ResultsFigure4.jpeg">
+<img width="100%" src="https://2019.igem.org/wiki/images/e/ec/T--Hamburg--ResultsFigure4.jpeg">
 <figcaption>
-<b>Figure 2: </b>Cell plated out on chloramphenicol agar plates. Left: Cells transformed with gate composition. Middle: Cells transformed with trigger 1 composition. Right: Cells transformed with trigger 2 composition.
+<b>Figure 4: </b>A) Cell plated out on chloramphenicol agar plates. Left: cells transformed with the gate plasmid. Middle: cells transformed with the trigger 1 plasmid. Right: cells transformed with the trigger 2 plasmid.
 </figcaption>
 </figure>
 </html>
-Due to leaking of the gate colonies could be found on plates were bacteria were transformed with the gate composition. In contrast, the single transformations with the trigger compositions were negative, as expected. For further information about the leakage visit <partinfo>BBa_K2970006</partinfo>.
+Unfortunately colonies also grew on the plates with just the individual transformation of the gate plasmid, though the number of colonies was much lower when compared to the transformation with all three plasmids. We sequenced the gate plasmid to confirm correct assembly. The results showed no mutation in the gate sequence. We concluded that the gate is showing signs of leakage, expressing the antibiotic resistance even in the absence of triggers. This basal expression was rather strong due to the strong promoter we used for our experiments.
+To measure the gates leakage, we observed cells transformed with all three plasmids on plates with different chloramphenicol concentrations and compared them to cells transformed with only the gate plasmid. As a positive control we used the <partinfo>pSB1C3</partinfo> backbone. The number of colonies per plate after twelve hours of incubation is shown in Figure 5.
+<html>
+<figure>
+<img width="100%" src="https://2019.igem.org/wiki/images/b/bd/T--Hamburg--ResultsFigure3.jpeg">
+<figcaption>
+<b>Figure 5: </b>A) Number of colonies per plate depending on the chloramphenicol concentration. <i>E. coli</i> DH5α cells were transformed with the gate plasmid (blue), the gate plasmid together with both trigger plasmids (red), or with the control backbone pSB1C3 (green). The colonies were counted after 12 hours.
+</figcaption>
+</figure>
+</html>
+The data clearly shows that the gate is leaking, but when compared to the triple transformation (red) and the control (green) the number of colonies when transformed with only the gate plasmid was significantly lower. Additionally the number of colonies when transformed with all three plasmids was larger than when transformed with the positive control.
+We also used a plate reader to measure the growth rate of cells that were transformed with three different plasmids (<partinfo>pSB1A3</partinfo>, <partinfo>pSB1C3</partinfo>, <partinfo>pSB1K3</partinfo> or <partinfo>BBa_K2970003</partinfo>, <partinfo>BBa_K2970004</partinfo>, <partinfo>BBa_K2970006</partinfo>) and compared it to cells without any plasmids. The results are shown in Figure 6.
+<html>
+<figure>
+<img width="85%" src="https://2019.igem.org/wiki/images/7/7e/T--Hamburg--ResultsFigure11.png">
+<figcaption>
+<b>Figure 6: </b>A) Plate reader growth curves of E. coli DH5&alpha;. The generation time was measured and calculated for non competent cells (orange), for cells transformed with the backbones pSB1A3, pSB1C3 and pSC1K3.M1 (blue), and for cells transformed with our two trigger plasmids together with the gate plasmid (green). Error bars show the standard deviation.
+</figcaption>
+</figure>
+</html>
+For cells transformed with three plasmids an impaired growth rate can be observed.
+We could not show that the transformation of our three plasmids was less harmful to the bacteria than the transformation with three different antibiotics, instead it shows comparable levels of stress.
+Due to the linker between the gate and our gene of interest (chloramphenicol acetyl transferase) additional bases were attached to the gene which might affect the functionality of the protein as it contained an additional 19 amino acids. To test the genes activity we inserted the sequence containing the additional bases into <partinfo>pSB1A3</partinfo>, transformed it into bacteria and plated the cells on chloramphenicol plates. The results of this experiment are shown in Figure 7.
+<html>
+<figure>
+<img width="100%" src="https://2019.igem.org/wiki/images/2/2a/T--Hamburg--ResultsFigure2.jpeg">
+<figcaption>
+<b>Figure 7: </b>Test transformation to check chloramphenicol resistance gene. E. coli DH5α cells were transformed with a test plasmid containing the modified chloramphenicol resistance gene (A). For negative control (B) pSB1A3 was used. For positive control (C) pSB1C3 was used.
+</figcaption>
+</figure>
+</html>
+Several colonies grew on the plate with bacteria transformed with the modified chloramphenicol acetyl transferase. The negative control showed no cell growth while on the plate with the positive control a cell turf has grown. This confirms that the activity of the chloramphenicol acetyl transferase was not significantly impaired by the additional amino acids.