Team:Kyoto/Project
1) Motivation
Protein interactions, enzymatic reactions, folding of RNA, riboswitches... nearly all of these biological reactions are greatly affected by salt concentation. Salt concentration is also important for most biological devices designed by synthetic biologists. Synthetic biologist try to develope new devices that provide solutions to our daily problems in the world. However, the situations and circumstances vary greatly among each problem, often resulting in undesired salt concentrations. If the salt concentration is insufficient in the surrounding environment for a developing device, adding salt to the culture solution may solve a problem.
But how about when salt concentrations are too high? This is a difficult problem to solve. Once devices that absorb salt from environment are developed, we can greatly support various functions of other devices, for example, sensing substances in the environment or bioremediation. Besides, if we can apply salt-absorbing device 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.
Although this has a great possibility, the question of how feasible is this environmental desalination using synthetic biology principles has never been explored thoroughly. Therefore, we addressed this problem this year.
2) Let's create a system that absorbs salt from a liquid using genetically modified yeast
Some salt-tolerant plants have developed systems that sequester Na+ from the cytoplasm to vacuoles in order to protect themselves from Na+ flowing in. In addition, some plants have gained Na+ tolerance system by producing compatible solutes. In the process of searching papers, we noticed that many genes involved in Na+ sequestration were also shown to function in budding yeast and give them salt tolerance. The budding yeast itself also has a mechanism for exporting Na+ out of the cell. It is also known that budding yeasts, in which Na+-exporting genes have been destroyed and the mechanism are failed, are very sensitive to the high salt concentration in the medium, suggesting that these genes contribute to salt-tolerance of budding yeast. Hence, we assume that if these mechanisms can be combined, it is possible to develope a "biological desalination" device that stores Na+ in the vacuoles of budding yeast and lowers the salt concentration of the environment.
We further investigated and noticed that team Aachen 2017, tried to create a similar budding yeast. We contacted the team Aachen and heard a detailed story. Here we proposed a question to ourselves. Can we combine genes of salt-tolerant plants and genes of salt-resistant and build a desalination system which team Aachen did not develop? We started to create budding yeast by expressing various genes and set "creating the device that minimizes the salt concentration of medium in the test tube" as the primary goal.
3) Aggregation system for increasing the efficiency of recollection and biosafety
As mentioned above, we initially aimed to create a yeast that removes salt in "test tubes" in order 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 in Human Practice, we have found a new goal that this system can also be used to solve the social problems such as a salt damage. In order to use our device in the real environment, we have to incorporate a mechanism that prevents genetically modified yeast from diffusing into the environment. For this purpose, we tried introducing an aggregation system to collect yeast efficiently after lowering the salt concentration in the environment.
4) Calculating the amount of yeast necessary to lower the concentration through mathematical modeling
The advantage of a salt removal system is that you can easily control the amount and combination of components because they are artificially defined. You can use different factors depending on the situations, such as a 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 etc. In order to enable this flexible application, it is necessary that our system is sufficiently understood, and mathematical modeling is properly done. By using the results of this modeling it is possible to estimate the optimalamount of yeast input when using our device.