Team:SYSU-Software/Partnership

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Overview

This year, we have maintained close cooperation with SYSU-China during the whole season.

Because of the recurrent COVID-19 epidemic, we keep in touch through both offline conferences and online communication. Our partnership has shaped our project in a fundamental and profound way.

- Beginning: similarities

After we have determined the core module, opto-controllable element designer, of our project, we find that although it is versatile, we still hope to add some tools to make it fully functional.

Then in the South China exchange meeting, we first found the similarities with SYSU-China. Their initial idea of the project was to use an RBP combined with a circle RNA, then use linker to connect the target protein with RBP, and achieve the aggregation of the target protein through the interaction between the RBP and the circle RNA, which in line with our original idea of the project that to gather the target protein together through photosensitive protein. These similarities laid the foundation for our cooperation.

Figure | our encounter during the South China exchange meeting

The iGEM opening ceremony gave us an opportunity for an offline conference, during which we conducted an in-depth discussion on the similarities between our project and how can we cooperate based on them. After this conference, we are both more convinced that both teams can provide help and advice to each other in this year's project, adding confidence to further cooperation.

Figure | our offline conference at the iGEM opening ceremony

- Middle: inspiration and design

When we were thinking about what kind of plug-in should be built for users to make the core of our software work better, SYSU-China proposed a hypothesis that we can gather the enzymes that catalyze the two-step reaction together in order to control a certain reaction. This idea is the source of our inspiration that we can link the enzyme with the light-sensitive protein, so as to achieve precise control of the reaction through light. In the later period, we cooperated with SYSU-China to turn this idea into reality.

Compared with SYSU-China, we have a deeper understanding of protein structure prediction and linker design. So we based on the needs of the experimental team and helped them find a specific linker. We selected several artificial linkers based on their protein conditions and verified the effect of the fusion protein on trRosetta, helping them optimize the experiment.

Figure | screenshot of the chat with Bingnan Zhao from SYSU-CHINA, discussing the linker selection problem

- Late stage: experimental verification

After the design of the entire software is basically formed, we have carried out a series of experiments to verify. During this period, we keep in touch with SYSU-China online and cooperate with them in many aspects of the experiment.

At the beginning, we tried to introduce two enzymes into the same E.coli, but after experimentation, this method was found to be inefficient. After online communication with our partner, we decided to modify the experimental protocol that we introduce the two enzymes into E.coli separately and then mix them after expression, which achieved good results. They also helped us to express light controlled GFP in mammalian cells.

In addition, SYSU-China used our structure prediction and activity selection algorithms to detect whether their products are functional as experimental verification.