Difference between revisions of "Part:BBa K3886003"

Figure 2: The design scheme of a caffeine–controlled genetic switch;

Figure 3: The response curve of caffeine–controlled genetic switch. Samples prepared in triplicate, data represent the mean ± 1 s.d.

Figure 4: The abstract scheme of the caffeine–controlled genetic switch in a cell. The caffeine nanobody-intein-ECF20 (NIE) is split separately, and then divided into two parts for expression. Then the input of caffeine will induce the recombine of split caffeine nanobody-intein-ECF20(NIE) protein (NIE), and then under the action of the intein, the split ECF20 will be recombined and the completed ECF20 will be released in the cytoplasm. Then the ECF20 will activate the pECF promoter and the expression of corresponding output.

* It describes the process of combining NIEα(1/2) protein and NIEβ(1/2) protein into NIE complex, and the breakdown of the NIE protein back into two separate parts.

* It describes the process that NIE binds to caffeine, forming a NIE-caffeine complex, which gradually turns in to ECF20 molecule and NI-Caffeine complex.

* It describes the process that NIE-caffeine complex gradually turns in to NI complex and Caffeine molecule.

Abbreviations

- NIE: Complex of Nanobody(acVHH)-Intein-ECF20

- NI: Complex of Nanobody(acVHH)-Intein

* Describe the protein expression of caffeine nanobody - intein -ECF20 (NIE) part α.

* Describe the protein expression of caffeine nanobody - intein -ECF20 (NIE) part β.

* Describe the protein production changes of caffeine nanobody-intein-ECF20 complex（NIE）.

* Describe caffeine concentration changes in the environment.

* Describe the protein concentration changes of the NI-caffeine complex.

* Describe the protein concentration changes of the NIE-caffeine complex.

* Describe changes in the levels of ECF20 protein in the environment.

* Describe the process of ECF20 activating mCherry mRNA expression.

* Describe the expression of mCherry protein.

Simulation Results and analysis

As can be seen from the results of the following analysis, the output of the caffeine sensor undergoes a rising at the beginning and then shows a decreasing trend after caffeine is completely consumed. Eventually, the output of the caffeine sensor gradually converges to 0 as the caffeine molecule is degraded or metabolized.

Figure 5: Trends of consumption of Caffeine molecules.

Figure 6: Trend of relative fluorescence intensity of mCherry with time

In our project, we plan to use the Hidro system as a delivery device for the oral cavity or intestinal tract to achieve the expression of drug molecules or health regulatory molecules by referencing common beverages such as coffee. In these scenarios, the caffeine-sensing switch needs to be able to respond effectively to caffeine and eventually turn off the switch after caffeine metabolism is complete.

The results of our mathematical simulations meet these expectations, and the model developed here will have the potential to guide actual dietary inputs to achieve the desired health modulation effects.

Application of the caffeine–controlled genetic switch based in Hidro system

In the project of NDNF_China 2021, we hope to help engineered strains work beyond the laboratory in a safe, stable and traceable way. So we present Hidro: a hydrogel system enclosing engineered bacterial strains. The outer layer of Hidro is a compact shell, offering both protection and containment, preventing the strains from escaping into the wild; the inner core of Hidro provides a supportive environment for them under harsh conditions, thus enabling their stable function; A genome-integrated Tracing and Control system offers tracking and specific killing of engineered strains in case of emergencies. We have experimentally demonstrated that Hidro can be implemented in diverse scenarios, such as heavy metal sensing, food-quality detection, drug secretion, etc. The Hidro system has the great potential to promote synthetic biology applications beyond the laboratory.

We first tested whether our caffeine–controlled genetic switch could be integrated into the Hidro system. After encapsulating engineered bacteria into Hidro beads and incubating with and without caffeine molecules respectively, we slice the beads at a thickness of roughly 0.5 mm. The sliced samples are then imaged with a fluorescence microscope under green light. It was confirmed visually that Hidro exposed to caffeine exhibited strong red fluorescence.

Figure 7: (A) The schematic of caffeine–controlled genetic switch encapsulated in the Hidro system; (B) The image of Hidro taken by a fluorescence microscope under green light.

The Hidro system has potential for safe drug delivery in food and the human gut (See more information in NDNF Proposed Implementation). So we then designed a caffeine–controlled L-Dopa production system based on the switch designed here (Figure 8A).

Derived from the biosynthesis of L-tyrosine (Figure 8B), L-Dopa is a naturally occurring amino acid that acts as a precursor to a number of neurochemicals such as adrenaline and dopamine. L-Dopa is an amino acid that is made and used as part of normal biological functions in humans.

We replace the output gene with L-Dopa metabolic pathway HpaB and HpaC, each with a specifically designed RBS (Figure 8A). After 24 hours of incubation in a tube, we removed the Hidro beads, centrifuged the liquid and took out the supernatant for L-dopa concentration measurement. From the result shown in Figure 8C, we can see that the Hidro group showed L-dopa production compared to those in the control group. It means that Hidro can realize the sensing and screting process. It further proves that Hidro has a great potential to be applied in Health.

Figure 8: (A) The schematic of caffeine–controlled genetic switch encapsulated in the Hidro system to produce L-dopa; (B) The metabolic pathway from L-tyrosine to L-Dopa. (C) L- Dopa concentration measurement in the caffeine–controlled L-Dopa production Hidro system.