Team:SZPT-CHINA/Engineering

Engineering

Overview

Engineering Success

BBa_K3740050

Design

Strategy

Experimental Results

BBa_K3740030

Design

Strategy

Experimental Results

Learning

BBa_K3740044

Design

Strategy

Experimental Results

Reference

● Overview:
The goal of project is to use optogenetically engineered Gluconacetobacter hansenii to fight with Pseudomonas aeruginosa infection and produce a bacterial cellulose dressing simultaneously. The genetic engineering consists of three modules, antipseudomonal drug production module, c-di-GMP signaling and BC film production module, safety and drug release module. We have so far made a lot of progress in this project. Hereby, we presented a summary of our engineering data. Although this project is still ongoing and improvements are needed to make in some sections, we believe that our work can contribute to the iGEM community.
● Engineering Success:
I. Antipseudomonal drug production module(BBa_K3740050
1. Design
We designed an antipseudomonal drug production module to specifically combat P. aeruginosa infection. The receptor domain, the translocase domain of pyocin S2 and the nuclease domain of colicin E3 are fused together to get a new chimeric bacteriocin termed SE. The antipseudomonal SE protein can target and inhibit P. aeruginosa, even including those harbouring a S2 immunity protein IMMS2. IMME3 is an immunity protein derived from Escherichia coli. It can bind to the nuclease domain of SE specifically and inhibit its activity, thus rendering the host cell immune to SE. A similar expression level of the antipseudomonal protein SE and the immunity protein IMM is designed to be expressed in the engineered bacteria, thus preventing the bactericidal effect of SE protein on the bacterial chassis itself.
2. Strategy
Two plasmids S2-PET28A and SE-PET28A were initially constructed and introduced into E. coli BL21. Following the induction of lysis protein by IPTG, bacterial cells were in turn disrupted and the supernatant containing the soluble SE proteins was collected. The molecular weight of SE protein was checked by SDS-PAGE while its specificity to P. aeruginosa was also verified using the drop plate assay; In order to improve the antipseudomonal effect, we engineered the RBS to modulate its strength in controlling SE protein expression. Finally, we identified pR-RBS300-SE-B1006-J23118-RBSII-IMM-rrnB T1(BBa_K3740050) as our optimal genetic circuit.
Figure 1. The gene circuit of pR-RBS300-SE-B1006-J23118-RBSII-IMM- rrnB T1 (BBa_K3740050)
3. Experimental results:
3.1 Sequencing
Plasmids from E. coli cells were extracted and sequenced. Analysis based on sequencing data indicated that the SE-encoded sequence and pR-RBS300-SE-B1006-J23118-RBSII-IMM-rrnB T1 (BBa_K3740050) have been successfully integrated into the plasmid vectors.
3.2 Characterization of fusion protein SE
3.2.1 SDS-PAGE
Method: IPTG was added to a final concentration of 0.1 mmol/mL to induce SE protein expression in E. coli BL21 and subsequently incubated at 25℃ for 12 hours. Supernatant containing SE or S2 proteins was obtained by sonication and centrifugation respectively. The crude protein extract was loaded into SDS-PAGE gel and stained by Coomassie Blue to verify the presence of target proteins (For more detailed steps, please click Experiments).

After induction by IPTG, S2 and SE protein expression in S2-PET28A-BL21 (lane 2) and SE-PET28A-BL21 (lane 3) has been identified. By contrast, target proteins were not expressed in the strain with S2-PET28A-BL21 (lane 1) and SE -PET28A-BL21 (lane 4) in the absence of IPTG, indicating that expression of S2 and SE proteins can be successfully induced in E. coli transformed with S2-PET28A and SE-PET28A, respectively.
Figure 2. SDS-PAGE analysis of protein expression in engineered E. coli BL21. Lane 1, S2-PET28A-BL21 without IPTG induction; Lane 2, S2-PET28A-BL21 with induction by 0.1mmol/mL IPTG; Lane 3, SE-PET28A-BL21 with induction by 0.1mmol/mL IPTG; Lane 4, SE-PET28A-BL21 without IPTG induction.
3.2.2 SE protein targeting verification
Method: Supernatant containing SE or S2 protein was respectively mixed with the culture of Pseudomonas aeruginosa PAO1, P. aeruginosa PAO1Δ1150-1151(PAO1 Δ1150-1151, PAO1 knocked out of S2+IMMS2) and E. coli MG1655. PBS was used as a negative control. Inhibitory effect of supernatant on the P. aeruginosa growth was determined by measuring OD600 using SYNERGY H1 micro-plate reader. (For more detailed steps, please click Experiments)

We found that the OD600 values of both P. aeruginosa strains cultured with SE protein, were much lower than that of the control group PBS. This proves that SE protein has antipseudomonal properties. In contrast, pyocin S2 could only act on the immune-deficiency strain PAO1∆1150-1151. This proves that SE protein has a broader antipseudomonal spectrum than S2. Meanwhile, the OD600 value of E. coli MG1655 cultured with SE protein was a little higher than that of the control group PBS. This indicates that SE protein does not work on E. coli. This result indicated that the fusion protein SE can specifically kill P. aeruginosa.
Figure 3. Optical density of bacterial culture of PAO1, PAO1 Δ1150-1151 and E. coli MG1655 treated by the supernatant of S2-PET28A-BL21 or SE-PET28A-BL21 for 790 minutes. PBS was used as the negative control.
3.3 Batch screening and verification of SE protein antibacterial performance of composite parts
Method: PAO1 growth inhibition verification. G. hansenii ATCC 53582 culture supernatant containing SE proteins that were expressed under control of different RBS were obtained by sonication and centrifugation and further purified by infiltration with micro-pored membrane. Then, supernatant in different groups was individually mixed with PAO1 culture, and incubated at 30℃ for 12 hours. SYNERGY H1 micro-plate reader was used to measure the OD600 to determine the effect on PAO1 growth. Inhibition zone experiment. 3μL of the supernatant containing SE protein was dropped on FAB plate with PAO1(For more detailed steps, please click Experiments).

As shown in Figure 4 (a), we found that the OD600 values of PAO1 strains cultured with supernatant of the 3rd, 4th, 7th, and 8th colonies bacterial lysate, were much lower than that of PBS in the control group. This proves that culture supernatant of the 3rd, 4th, 7th, and 8th colonies had a remarkable inhibitory effect on the growth of PAO1. Consistent with this result, supernatants from all the G. hansenii isolates have formed inhibition zone on the plate spread with PAO1, yet with different sizes. The 3rd and 4th isolate displayed the most significant antipseudomonal effect, while the control, the 9th colony had no effect. Taken together, these results show that expression of SE protein was successfully induced in G. hansenii ATCC 53582. Besides, by adjusting the RBS upstream the SE-encoded sequence, we screened and identified that the 4th strain, pR-RBS300-SE-B1006-J23118-RBSII-IMM-rrnB T1-pSEVA331-G. hansenii ATCC 53582-4# exhibited the optimal antipseudomonal effect.
Figure 4. (a) Optical density of bacterial culture of PAO1 treated by the supernatant of engineered strains for 790 minutes. (b) Inhibition zone test. (c) Strains are used for Figure(a) and Figure(b).
3.4 Video shooting
Video 1. Video shooting of the zone of inhibition of 4th bacteria: pR-RBS300-SE-J23118-RBSII- IMM-rrnB T1-pSEVA331-G. hansenii ATCC 53582-4#.
II. C-di-GMP signaling and BC film production module (BBa_K3740030)
1. Design
This c-di-GMP signaling and BC film production module has two submodules. One is the diguanylate cyclase sub-module, which regulates the synthesis of c-di-GMP. The bacterial phytochrome BphS is utilized to synthesize c-di-GMP in a light-dependent manner, thereby controlling BC film production in G. hansenii ATCC 53582. The other is c-di-GMP phosphodiesterase sub-module, which regulates the hydrolysis of c-di-GMP. By screening different parts, the level of c-di-GMP in bacteria can remain in a low level or even close to zero under the dark condition.
2. Strategy
A series of plasmids derived from J23100-B0034 were constructed and transferred into G. hansenii ATCC 53582, in which the BC film production was quantified. Finally, fcsR (BBa_K3740022) was selected as the c-di-GMP phosphodiesterase encoding gene. Different promoters were then used to direct the expression of FcsR. Based on the screening results, BBa_K3740030, BBa_K3740031 and BBa_K3740043 were constructed and introduced into G. hansenii ATCC 53582 through electroporation. Finally, BC film production was assessed in these strains.
Figure 5. The gene circuit of J23100-B0034-bphS-pET RBS-bphO-rrnB T1-J23109-B0034-fcsR- rrnB T1 (BBa_K3740030).
3. Experimental results
3.1 Agarose gel electrophoresis
As shown in Figure 6 (a), c-di-GMP phosphodiesterase-encoded genes (BBa_K3740065), (BBa_K3740062) and (BBa_K3740066) were identified successfully by PCR amplification and c-di-GMP diguanylate cyclase-encoded genes (BBa_K3740047) was identified by PCR amplication; As shown in Figure 6(b), composite parts including (BBa_K3740030), (BBa_K3740031) and (BBa_K3740043) were identified successfully by PCR.
Figure 6. (a), (b)The agarose gel electrophoresis image of the constructed plasmid after PCR amplification. (c)Plasmids are used for Figure(a) and Figure(b).
3.2 Film production verification experiment
3.2.1 Film production verification experiment of bphS and fcsR
Method: The constructed plasmids were introduced into G. hansenii ATCC 53582 and cultured at 30°C. Then a single colony was picked to launch its liquid culture. Then the culture was distributed in two copies of 12-well plates, with one under NIR light illumination and the other under dark condition for 4 days. (For more detailed steps, please click Experiments)

As shown in Figure 7 (a), BC production in J23100-fcsR-rrnB T1-pSEVA331- G. hansenii ATCC 53582 and the control group pSEVA331- G. hansenii ATCC 53582 were different, indicating that FcsR was capable of hydrolyzing c-di-GMP in G. hansenii. While, J23100-bphS-pET RBS-bphO-rrnB T1-pSEVA331-G. hansenii ATCC 53582, produced a higher level of BC film under near-infrared light than that under dark condition, indicating that BphS in G. hansenii ATCC 53582 can synthesize c-di-GMP. To summarize, BphS and FcsR were opted as the c-di-GMP synthetase and hydrolase in our system, respectively.
Figure 7. (a)BC yield by J23100-B0034-fcsR-rrn B T1-pSEVA331-G. hansenii ATCC 53582, J23100-B0034-yhjH-rrnB T1-pSEVA331-G. hansenii ATCC 53582, J23100-B0034-rocR-rrnB T1-pSEVA331-G. hansenii ATCC 53582 and the vehicle control pSEVA331-G. hansenii ATCC 53582; (b) BC yield by J23100-bphS-pET RBS-bphO-rrnB T1-pSEVA331-G. hansenii ATCC 53582 under NIR light illumination and dark condition.
3.2.2 Film production verification experiment of bphS-fcsR
A significant difference in BC film production under NIR light and dark conditions were observed for those strains, including J23100-B0034-bphS-pET RBS-bphO-rrnB T1-J23109-B0034-fcsR-rrnB T1-pSEVA331-G. hansenii ATCC 53582, J23100-B0034-bphS-pET RBS-bphO-rrnB T1-J23110-B0034-fcsR-rrnB T1-pSEVA331-G. hansenii ATCC 53582, however J23100-B0034-bphS-pET RBS-bphO-rrnB T1-J23119-B0034-fcsR-rrnB T1-pSEVA331-G. hansenii ATCC 53582 had no difference in BC film production under NIR light and dark conditions, these results showed that J23100-B0034-bphS-pET RBS-bphO-rrnB T1-J23109-B0034-fcsR-rrnB T1-pSEVA331-G. hansenii ATCC 53582 and J23100-B0034-bphS-pET RBS-bphO-rrnB T1-J23110-B0034-fcsR-rrnB T1-pSEVA331-G. hansenii ATCC 53582 can be used as our gene circuit.
Figure 8. (a) BC film production by different strains, (b) Strains are used for Figure(a).
3.3 Video shooting
Video 2. Video shooting of J23100-B0034-bphS-pET RBS-bphO-rrnB T1-J23109-B0034-fcsR-rrnB T1-pSEVA331-G. hansenii ATCC 53582 bacterial BC production.
4. Learning:
In our film production assay, the film production by engineered bacteria under dark condition was expected to remain at a very low level. Surprisingly, a substantial amount of BC film was still found without NIR light induction, even though the level was lower than that in the NIR-induced group. In the future, we will solve this problem and refine the genetic circuit.
III. Safety and drug release module (BBa_K3740044)
1. Design
This module is a dual design of both safety control and drug release. We use pDawn, a blue-light-responsive promoter to direct the expression of the lytic proteins, which would cause the lysis and death of the engineered bacteria. Then, SE protein expressed within the engineered bacteria will be released. We have constructed a set of plasmids which include pDawn to induce the expression of an anti-holin-free Lambda lysis cassette (S105), φX174 lysis gene (X174 E), and LKD16 lysis cassette (LKD16). They were chosen to lyse our chassis bacteria. After screening, X174 E (BBa_K2656015) was selected as the final part in our safety and drug release module.
2. Strategy
RFP was firstly used to verify the responsiveness of the pDawn promoter to blue light. Then, random primer guided mutagenesis method to modulate the strength of the RBS (BBa_B0034) located upstream of X174 E. Finally, the pDawn-RBSNNN-X174 E-rrnB T1 (BBa_K3740044) plasmid was constructed and introduced into E. coli. E. coli isolates that grow normally in the dark and cannot grow under blue light were screened out. Finally, the plasmid was extracted, and further introduced into G. hansenii ATCC 53582, in which the responsiveness of pDawn to blue light was also verified.
Figure 9. The gene circuit of pDawn-RBSNNN-X174 E-rrnB T1 (BBa_K3740044).
3.Experimental results
3.1 The pDawn promoter responds to blue light verification in G. hansenii ATCC 53582
Red fluorescence could be observed in the pDawn-B0034-RFP-rrnB T1-pSEVA331-G. hansenii ATCC 53582 under 470-nm blue light, but there was no red fluorescence under dark condition, suggesting that the pDawn promoter could respond to blue light and induce gene expression in G. hansenii ATCC 53582.
Figure 10. Red fluorescence photo of the pDawn-B0034-RFP-rrnB T1-pSEVA331-G. hansenii ATCC 53582 cultured under 470-nm blue light (a) or dark condition (b) for 24 hours.
3.2 Batch screening of pDawn-RBSNNN- X174 E-rrnB T1-pSEVA331 in response to blue light lysis in E. coli
Method: We use the random primer method to modulate the strength of the RBS (BBa_B0034) located upstream of X174 E. After introducing into E. coli DH5α, a drop plate assay was performed to screen the bacterial isolate that can grow normally in the dark but cannot under the blue light irradiation.

As shown in Figure 11, the 4th isolate that grew normally in the dark but did not under blue light, indicating that we successfully expressed the cleavage protein X174 E in E. coli.
Figure 11:The growth status of pDawn-RBSNNN-X174 E-rrnB T1-pSEVA331-DH5α under blue light (a) and dark condition (b).
3.3 pDawn-RBSNNN-X174 E-rrnB T1-pSEVA331-7# in response to blue photolysis in G. hansenii ATCC 53582
Method: We launched the liquid culture of pDawn-RBSNNN-X174 E-rrnB T1-pSEVA331-DH5α, extracted the plasmid and introduced into G. hansenii ATCC 53582. After 2 days of incubation, we selected 20 monoclonal to spot on two parallel new plates, which were incubated for another 2 days, with one under blue light and the other in the dark. The strains with obvious growth difference under different illumination conditions were preserved. The drop plate assay using this strain was repeated to verify the lysis effect of X174 E on G. hansenii ATCC 53582.

As shown in Figure 12 (a), G. hansenii ATCC 53582 strains under the dark condition exhibited better growth than those under blue light irradiation; (b) pDawn-RBSNNN-X174 E-rrnB T1-pSEVA331-G. hansenii ATCC 53582-7# showed a stable lysis effect under blue light illumination but not in the dark, indicating that we successfully expressed the cleavage protein X174 E in G. hansenii ATCC 53582.
Figure 12. (a) The growth status of pDawn-RBSNNN-X174 E-rrnB T1-pSEVA331-G. hansenii ATCC 53582-4# under blue light (1) and dark conditions (2), (b)The growth status of pDawn-RBSNNN-X174 E-rrnB T1-pSEVA331-G. hansenii ATCC 53582-7# under blue light (1) and dark conditions (2).
In our safety and drug release module, we verified the lysis effect of (BBa_K3740024) and (BBa_K3740032), however their effect was inferior to that of (BBa_ K2656015). If you are interested in our other two parts, please Click: (BBa_K3740033) and (BBa_K3740051).
Reference
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