Designing a Customizable Synthetic Cell Compartment Toolbox
Have you ever looked at an airplane and thought about how intricately each part has to be designed to fit into the overall machine?
Engineers have long used the technique of designing, testing and redesigning components of larger machines in order to improve them. Because they understand every detail of the machine they are able to accurately predict the behavior of each part. This has lead to the development of ever-more useful tools.
Every Biologist dreams of being able to utilize this process with the same efficiency. They spend a whole lot of time planning the part and its function in the respective organism. Then they integrate the part and find out that it either doesn't work, kills the cell, or causes unexpected reations. This is because most of the time the organism is not completely understood and there is interference with some part of the natural metabolism. Our aim is to solve this problem! Our team, "artico", which stands for artificial compartments, has created a fully customizable cell compartment toolbox which can be used to create a reaction room inside a cell tailored exactly to the user's needs. Our compartment can import proteins specifically chosen by the user, change its luminal environment as well as its size, and secrete its content to the extracellular medium. It can be used for a wide variety of purposes, be it basic research, compartmentation of toxic metabolic pathways, or even more exotic functions such as in vivo protein crystallization.
Medal Criteria
Bronze
Register And Attend
- Thanks to the amazing support of both universities and our friends and sponsors, our team was successfully registered and is looking forward to conclude an amazing year at the Giant Jamboree!
Deliverables
- We created our own wiki and are excited for everyone to explore our work!
- We are very proud of what we have achieved as a team and we are also happy to present everyone who attributed to our success!
- We are looking forward to inspiring discussions at our poster during the Giant Jamboree!
- We worked very hard on an exciting presentation and look forward to showing what we have achieved!
- We have thoroughly discussed safety and security issues associated with our project and have documented the results in our Safety Forms!
- We documented all created and submitted parts and submitted DNA samples to the registry!
- We have submitted the following parts.
Attribution
- We are very thankful for all the support we experienced during the competition and are more than happy to mention everyone who attributed to our project and wiki!
Characterization / Contribution
- We have successfully participated in the InterLab Measurement Study and submitted our data in time
Silver
Validated Part / Validated Contribution
- We characterized BBa_K2271060, BBa_K2271103, BBa_K2271066 and BBa_K2271062.
- These parts were submitted to the iGEM registry and are experimentally validated
Collaboration
- We were delighted to meet other teams and collaborate in order to achieve our goals
Human Practices
- One of the most valuable experiences of the competition was sharing our project and acquired knowledge with the public. We highly enjoyed inspired conversations about ethical and societal aspects of synthetic biology, organizing our own SynBio conference, and starting a worldwide postcard campaign!
Gold
Integrated Human Practices
- In addition to engaging with the public, we expanded our Human Practices by investigating both ethical and scientific issues, opportunities and limitations of our projects. Meeting experts from both international laboratories and companies as well as representatives from ethical references centers, we were happy to integrate their valuable feedback into our lab work!
Improve a previous part or project
- We are proud to improve roGFP (BBa_K1093013) of Team iGEM13_Warsaw with our part (BBa_K2271024). In order to use the redox sensing in vivo sensor we optimized it for our application in yeast.
Model your project
- Prior to conducting experiments about enabling full control over the peroxisomal protein import we predicted the structure for the yeast peroxisomal matrix import protein using AMBER and VMD. Additionally, we modeled the nootkatone pathway to optimize our proof-of-concept and show the advantages of cellular compartmentation using python.
Demonstrate your work
- We were able to show our functional proof of concept under real world conditions
Special
We have done some really good work so we applied for these Special Prices:
Results |
Achieved |
|---|---|
| We were able to design and successfully test an orthogonal peroxisomal protein import mechanism for peroxisomes in S. cerevisiae |  |
| By decorating the peroxisomes with the v-SNARE Snc1 we successfully secreted their entire contents | |
| With two different sensors we were able to efficiently measure the pH and the redox potential inside our yeast peroxisomes | |
| Via fluorescence microscopy we verified that the integration of new membrane proteins into the peroxisomal membrane is possible | |
| By successfully translocating the required enzymes for the metabolic pathways of Nootkatone and Violacein into the peroxisome and actually synthesizing the latter, we developed a proof of concept for our toolbox | |
| We successfully implemented a way of customizing the size and number of the peroxisomes into our toolbox | |
| With a high throughput assay we characterized the import efficiency of different PTS2 sequences | |
| To get a better understanding of possible problems and pitfalls of our metabolic engineering concepts we extensively modeled the whole nootkatone pathway and the benefits of it being translocated inside our compartment | |
| For our planned optogenetic experiments we designed an affordable lightbox which can easily be assembled in a short time | |
| All our excellent results can be combined into a highly variable compartment toolbox for designing artificial compartments based on the peroxisomes in S. cerevisiae with an enormous range of applications | |
