Team:Kyoto/Project
1) Motivation
Protein interactions, enzymatic reactions, folding of RNA, riboswitches... nearly all of these biological reactions are greatly affected by ionic strength. Most devices used for synthetic biology are also subjected to similar limitations. Synthetic biology faces our daily challenges and aims to develop new devices that provide solutions to every situation, every environment, and every problem that exists in the world. When the salt concentration is insufficient in the surrounding environment of a developing device, it may be possible to solve it by adding salt to the culture solution.
But how about when salt concentrations are too high? This is more a difficult problem to solve. Once devices that absorb salt are developed in a certain environment containing strong salt concentration, we can greatly support various functions of other devices, for example, sensing of substances in the environment and bioremediation. Besides that, if we can apply it to the situation outside the laboratory, there is a possibility that it will be useful for purifying water in various scenes such as industrial wastewater and salt damage.
How achievable is environmental desalination using synthetic biology principles? This question has never been explored sufficiently, so we addressed this problem this year.
2) Let's create a system that absorbs salt from a liquid using genetically modified yeast
In certain salt-type plants, they developed a system that sequesters Na+ from the cytoplasm to vacuoles in order to protect themselves from Na+ flowing in. In addition, some plants retain Na + tolerance system by producing compatible solutes. In the process of searching papers, we noticed that many genes involved in Na+ sequestration also function in budding yeast and give salt tolerance. The budding yeast itself also maintains a mechanism for releasing Na+ out of the cell, and it is also known that in some budding yeasts in which those genes have been destroyed and the mechanism failed, they are very sensitive to the salt contained in the medium. If these mechanisms can be combined, it is possible that a "biological desalination" device that stores Na+ in the vacuoles of budding yeast and lowers the salt concentration of the extracellular fluid.
We further investigated and we noticed that team Aachen 2017, created a similar budding yeast. We contacted the team Aachen and received a detailed story. Here we proposed a question to ourselves. Can we combine genes of salt plants and genes of salt-resistant soy sauce yeasts and build a desalination system which team Aachen did not develop? We started to create budding yeast by expressing various genes and set "the device that minimizes the salt concentration of medium in the test tube as much as possible" as the primary goal.
3) Aggregation system for raising the efficiency of recollection and biosafety
As mentioned above, we initially aimed to create a yeast that removes salt in "test tubes". As a result, we assumed to promote the usage of the biosensor, which detects trace elements contained in test samples such as blood and waste liquid, without being inhibited their function by salt in solution. However, from the activities at Human Practice, we have found a new goal that this system can also be used for social problems such as to stop the problem of salt damage. Assuming such a case, we have to incorporate a mechanism that prevents genetically modified yeast from diffusing into the environment. For this purpose, we tried introducing a new aggregation system as a system for collecting yeast more efficiently.
4) Calculating the amount of yeast necessary to lower the concentration through modeling
The advantage of a salt removal system with artificially placed defined components is that you can operate the amount and combination of these components freely. You can use different factors depending on the situation, such as the difference in initial salt concentration of an extracellular fluid, a difference in target salt concentration, a difference in time required for salt concentration manipulation, a difference in a required amount of yeast and more. In order to enable this flexible application, it is necessary that the system to be used is sufficiently understood, and modeling is done mathematically. By using the results of this modeling it is possible to estimate the optimal initial yeast input when using the device of this study.