Difference between revisions of "Part:BBa K2240000"

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AHL sensor with positive feedback loop, GFP output and antisense RNA type 1 inhibition

This part can detect the deliberately released stimulus so as to initiate the process of 'knockout'. Considering that the released stimulus can be diluted in an environment, a positive feedback loop is introduced to amplify the signal. 3OC6HSL, which is a member of acyl-homoserine lactone (AHL) family, would be the inducer. 3OC6HSL originated from V. fischeri is a lipid molecule that can diffuse through bacterial cell membrane to facilitate the cell-to-cell communication.

This part begins with the TetR repressible promoter (BBa_R0040), which can act as a constitutive promoter of the downstream protein - LuxR (BBa_C0062) under the absence of repressor TetR. Once the 3OC6HSL is added, LuxR will form a complex with 3OC6HSL and then activates the downstream promoter, P_luxR (BBa_R0062). In the end, the production of LuxR can be boost, allowed by the accumulation the LuxR.

After the activation of P_luxR, the autoinducer synthetase (BBa_C0061) would synthesize 3OC6HSL, which would bind to LuxR, from S-adenosyl-L-methionine (SAM) in cell. Due to the increase of the 3OC6HSL/LuxR complex, the entire part starting from P_tetR to LuxI generates positive feedback loop, hence further induces the P_luxR. Apart from this, the 3OC6HSL molecule can also diffuse to the extracellular environment and induce the cells nearby.

Owing to the positive feedback loop, this part would start contributing to signal emission whenever it receives 3OC6HSL molecules. As a result, it is expected to elevate the efficiency of activation under induction.

Considering the difficulties that previous iGEM teams encountered - the leakiness of P_luxR (See experience in BBa_F2620), we tried to get rid of this by adding antisense RNA Binding regions and antisense RNA (asRNA), interaction of which, could counteract the activity of basal level. Ideally, this could help tackling the thorny issue.

Usage & Biology

The antisense RNA (asRNA) had two important characteristics which might help boost the efficiency in reducing leakiness: possessing the sequence complementary to the mRNA of ABR, and a Hfq (RNA binding protein) binding site. The affiliation of asRNA to the complementary ABR would prevent ribosome from binding to the mRNA of the targeted RBS. Meanwhile, the presence of a Hfq binding site would help reduce the translation of the 3OC6HSL/LuxR complex since Hfq binding site was suspected to recruit RNase to degrade the targeted RNA chain. With these two effects, the leakiness of P_luxR could be lowered.

There are two asRNAs binding regions (ABR) in total. One is placed right before the targeted ribosomal binding site (RBS), which is upstream of the autoinducer synthetase for AHL (BBa_C0061) and GFP generator (BBa_E0240).

Under the presence of the 3OC6HSL, 3OC6HSL/LuxR complex could repress P_luxL, reducing the production of the asRNA, in turn increasing the production of LuxI. This means that the maximum level of LuxI translation could be achieved after 3OC6HSL induction.

Based on the reasons above, it is expected that the system would become more sensitive due to the positive feedback loop, whereas the promoter leakiness could also be reduced.

Antisense RNA Type 1 & 2

To provide an alternative, two antisense RNA sequences (type 1 and type 2) with a few base pairs different were designed. Both of them were obtained from the paper, Development of design rules for reliable asRNA behavior in E. coli, and they were then slightly modified. Being incorporated into an inducible system with positive feedback loop (PFB) that was able to produce GFP, they could be evaluated for their efficiency in reducing the basal level via measuring the GFP output under the presence of AHL.

Fig.1 Error bar presents SD from 6 biological replicates.

Fig.2 Error bar presents SD from 6 biological replicates.

Constructs involved

1. w/o PFB (with positive feedback loop): pSB1C3-BBa_T9002
2. w/ PFB (without positive feedback loop): pSB1C3-BBa_F2620-C0261-E0240
3. PFB + asRNA1: pSB1C3-BBa_K2240000
4. PFB + asRNA2: pSB1C3-BBa_K2240003

Finding 1. Antisense RNA (asRNA) can reduce basal expression level

The efficiency of basal level reduction for asRNA type I and II were compared with the control (w/PFB) prior to AHL induction ([AHL]=0M) and after the induction ([AHL]=1.00E-05 M). Unpaired t-test analysis suggested that their differences could be considered as highly statistically significant. Therefore, the two asRNAs could effectively lower the basal level of the targeted promoter.

Finding 2. Antisense RNA type II reduces basal level more significantly

Based on the results obtained from the unpaired t-test calculation, there were significant differences between antisense RNA type I and type II under both cases - before and after AHL induction (1.00E-05 M). Fig.1 and 2 implied that construct with asRNA type II could reduce basal expression level more significant than asRNA type I. It was conjectured that this might be caused by the GC content difference in their complementary sites (55% for asRNA type II comparing to 47.4% for asRNA type I) since the two asRNAs only differed in their GC content and sequences.

Signal Amplification

GFP was measured in order to examine the efficiency for the positive feedback loop to amplify the signals with the presence of the AHL inducer.

Fig.3 Error bar presents SD from 6 biological replicates.

Fig.4 Error bar presents SD from 6 biological replicates.

Finding 3. Positive Feedback Loop works after AHL induction

There were also notable statistical differences when comparing the changes before and after induction using the two-tailed paired t-test analysis for both PFB+asRNA1 (p<0.001) and PFB+asRNA2 (p<0.01). The average of fluorescence/OD600 for PFB+asRNA2 was 4,199.18 while the average after its induction was 6,121.58, showing an increase for around 2,000 GFP/OD600 (45.8% growth) after 3 hours. On the other hand, PFB+asRNA1 also experienced an increase by 4,765 GFP/OD600 (65.7% growth) under the same condition (Fig.5), suggesting that asRNA could regulate translation inhibition more tightly. This showed that there should be an increase in expression after the AHL induction.

Conclusions from the Experiments

The antisense RNAs construct can verify the following hypotheses:

1. There was a significant decrease in basal level when antisense RNA type I and II were incorporated into the system.

2. Antisense RNA type II reduced basal level more efficiently than antisense RNA type I.

3. Positive feedback loop was functional after being activated by 1.00E-05 M of AHL for 3 hours.

Sequence and Features