Part 3: Biosafety
Cycle 1
● Design
In order to verify how strong the quorum sensing promotors Plux、Plas are and to explore a proper concentration to induce them, we designed two plasmids: Plux-deGFP and PLas-deGFP, using the plasmid pET28a as the backbone.
In Plux-deGFP plasmid, full-length deGFP(green fluorescence protein) is fused with a Plux. Moreover, we use T7 promotor to express transcription factor LuxR. Then, promotor Plux is activated by LuxR which is binding with another external quorum sensing N-acyl homoserine lactones (AHLs) Lux 3OC6 Once expressed, the protein deGFP can be excited to green fluorescence and thus be detected by Fluorescence microplate reader.
The PLas-deGFP plasmid nearly works the same as PLux-deGFP plasmid, except that the promotor Plas is activated by the LasR coexisting with Las AHL.
Fig. 29 genetic circuit of PLux-deGFP and PLas-deGFP
● Build
For PLux-deGFP, LuxR-PLux-deGFP was synthesized by Genscript and subcloning was performed to get the final product.
Fig. 30 Map of Plux-deGFP
For PLas-deGFP, LasR-PLas-deGFP was synthesized by Genscript and subcloning was performed to get the final product.
Fig. 31 Map of PLas-deGFP
● Test
Plasmids were transformed into E. coli BL21(DE3) separately. Sequencing verifies transformation success.
Fig. 32 Sequencing of PLux-deGFP and PLas-deGFP transformants
Fluorescence microplate reader tests were conducted to verify the protein expression in engineered bacteria. The fluorescence intensity of induced promoter expression was measured in a bivariate between the concentration of the AHLs solution and the induction time. To see more details, visit the
Results page.
● Learn
During our testing process, we found that there was a gradient of fluorescence intensity with the gradient difference in induced concentration of the AHLs and time, and the gradient was in line with our expectations.
What's more, some lptE groups showed a high level of leaking expression of deGFP, which is embodied in the fluorescence intensity. We suspect that in E. coli, there exist other AHLs to affect the activation of Plux and Plas.
From this cycle, we had a better understanding of the Lux system and the Las system, which will guide us in the following cycle.
Cycle 2: CcdA&CcdB verification
● Design
After verifying the functionality of the QS system, we further tested the toxicity of CcdB and the detoxification ability of CcdA. In this cycle, we chose Pet-28a as our backbone and designed one plasmid: CcdB_CcdA. In the plasmid, CcdB is expressed by the T7 promoter, while CcdA is under the control of araBAD promoter, which is triggered by L-arabinose. All transcription processes are terminated by double terminators.
Fig. 33 The genetic circuit of CcdB_CcdA
● Build
In plasmid CcdB_CcdA, the designed fragment was synthesized by Genscript, and subcloning was performed to obtain the final product.
Fig. 34 The map of CcdB_CcdA
● Test
During the test process of this cycle, we encountered various problems. The initial problem was transformation. The fact that CcdB was toxic to E. coli and the lac operator was leaking made it difficult to transform the plasmid into E. coli BL21(DE3). After a month's try, we eventually selected another strain E. coli Tuner(DE3)pLysS, and successfully transformed the plasmid into the strain.
Fig. 35 Sequencing success for CcdB_CcdA transformant.
After the transformation, we conducted 2 sets of experiments: CcdB toxicity verification and CcdA detoxicaiton verification. To see more details, visit the
Results page.
● Learn
Firstly, to express a type of protein that is toxic to the host, strain selection must be carefully considered. We chose E. coli Tuner(DE3)pLysS instead of E. coli BL21(DE3) to obtain the transformants. The protein expression level of Tuner series strains can be precisely regulated by IPTG concentration, with strict concentration dependence. The pLysS plasmid can produce T7 lysozyme, which can effectively reduce the basal expression level of the target gene.
Secondly, the IPTG gradient didn't strictly echo with the OD600 gradient. But there was a turning point between 103μM and 102μM. From 103μM to 102μM, bacteria underwent a growth inhibition state to a normal growth state. In contrast, the result of the L-arabinose gradient didn't show this phenomenon. The L-arabinose gradient was in line with the OD600 gradient well, except the final OD600 in 10g/L L-arabinose was lower than 1g/L. We hypothesized that 10g/L was too high, adding extra metabolic stress to the bacteria and leading to cell death.
Based on this cycle, we better understood the toxicity and detoxication effects of CcdB and CcdA, which will guide us in the following cycles.
Cycle 3
● Design
After verifying the functionality of basic parts
(LuxR/LuxI system, LasR/LasI system, CcdA&CcdB), we design an exogenous verification
experiment. In this cycle, we combined the QS and CcdA/B toxin-antitoxin systems.
We designed two plasmids: Exo_LuxR and Exo_LasR, using pBAD_hisA as the backbone.
Fig. 36 The genetic circuit of Exo_LuxR
In Exo_LuxR, CcdB is activated by araBAD promoter, which is induced by L-arabinose. CcdA is controlled by promoter Plux. Promoter J23106 constitutively expresses LuxR. All gene transcription processes are terminated by double terminators(BBa_B0015). In this circuit, when we add arabinose into the medium, the transformed bacteria will be killed by the expression of CcdB. When we add 3OC6, CcdA will be expressed and prevent the toxic effect of CcdB.
In Exo_LasR, LasR is expressed by araBAD promoter, while CcdB is expressed by Plas.
All the processes of transcription are terminated by double terminators(BBa_B0015).
When we add 3OC12HSL and L-arabinose, the engineered bacteria will be killed by the
expression of CcdB.
Fig. 37 The genetic circuit of Exo_LasR
● Build
For both Exo_LuxR and Exo_LasR, the designed fragments were synthesized by Genscript, and subcloning was performed to obtain the final product.
Fig. 38 Map of Exo_LuxR and Exo_LasR
● Test
The test of this cycle was not as expected.
For Exo_LuxR, we successfully transformed the plasmid into E. coli Tuner(DE3)pLysS. The sequencing result was as follows.
Fig. 39 Sequencing success of Exo_LuxR transformants
However, we tried several methods to verify the functionality of the plasmid, all gaining unsatisfying results. Initially, we tried to measure OD600 changes over time. We tried the L-arabinose gradient and 3OC6HSL gradient, but all showed no obvious difference in the growth of bacteria.
Fig. 40 OD600changes overtime in L-arabinose gradient and 3OC 6HSL gradient
We also tried the CFU method and the trypan blue staining method. In the CFU method, we found no obvious difference between the situation of induction and without induction. In the trypan blue staining method, we found almost all bacteria that appeared in the field of view were alive.
For the time limitation, we didn't conduct testing for the Exo_LasR plasmid.
● Learn
Aiming at figuring out the problem, we discussed it with our advisors Jincheng Wang and Zixuan Ding.
We initially talked about the design of the plasmids. Since all parts were verified in the previous cycle, the sequence wasn't the source of problem. The only difference was that this time, CcdB was expressed under the control of araBAD promoter instead of the T7 promoter. We applied this change due to the finding of leakage of the T7 promoter in the previous cycle and cycle 1 in the Secretion subgroup. We assumed that the strength of araBAD promoter was too weak to express a sufficient amount of CcdB. In the following experiment, we will try to change the promoter.
What's more, since CcdB is toxic to bacteria, it might have random mutations in the sequence during the propagation. We then conducted PCR, using bacteria incubated for 2 weeks as templates. The sequencing result showed that the sequence of CcdB was complete.
Fig. 41 Sequencing result for Exo_LuxR, using bacteria incubated 2 weeks as templates
Cycle 4
● Design
While we designed the exogenous QS verification, we also designed the endogenous verification experiment. In this cycle, We designed two plasmids: LuxR_LasI and LasR_LuxI, using pBAD_hisA as the backbone.
The overall genetic circuits of these two plasmids are similar to exogenous systems. But this time, the quorum sensing substances are synthesized by bacteria. In LuxR_LasI, LasI is expressed, which will synthesize 3OC12HSL. In LasR_LuxI, LuxI is expressed and synthesize 3OC6HSL. Therefore, bacteria transformed with these plasmids separately will secrete quorum sensing substances and activate the genetic circuit of each other.
Fig. 42 the genetic circuit of LuxR_LasI and LasR_LuxI
● Build
For both LuxR_LasI and LasR_LuxI, the designed fragments were synthesized by Genscript and subcloning was performed to obtain the final product.
Fig. 43 The map of LuxR_LasI and LasR_LuxI
● Test
Due to the time limitation, we were unable to test the endogenous system.