Team:OUC-China/Description

Team OUC-China: Main

Overview

When we started

The genome contains commands which help the cell realize some basic functions like assimilation, reproduction, communication, motility and dissimilation. Cells also can be programmed by exogenous DNA which have new commands that guide the cell to perform new artificial tasks and aims in parallel. As we all know, synthetic biology developed very fast in recent years. One of the most important things that helps us to build our fantastic dream in synthetic biology is to develop small modular genetic parts. By doing this, the function of artificial circuits will become more predictable and easier to operate. Genetic engineering is reaching a new stage where microorganisms can be programmed by synthetic constructs. More and more toolbox of modular genetic parts is designed to interface with the control of cellular processes. The gene regulation tool for controlling and remodeling of circuits is essential and valuable.

The existing strategies

To satisfy various requirements, scientists have already created a lot of gene regulation tools based on three levels: DNA, RNA and protein. Among above three levels, post-transcriptional regulation plays a critical role for gene expression control. Post-transcriptional regulation generally refers to the control on RNA molecules. There are several advantages of post-transcriptional regulation comparing with traditional genetic regulation methods on DNA, like faster response time, simpler regulatory mechanism and diverse design strategies. More and more methods have been created based on post-transcriptional regulation because of its flexibility and practicability [1][2][3].

A typical case is riboswitch which can bind to a small molecule and result in a secondary structure change of mRNA with translation rate tuning of corresponding protein. It is not only a potential biosensor design platform, but also a powerful tool to control the expression level of downstream genes.

RNA switch responsive to small RNA is another type. Small RNA could also be engineered as an activator, which is able to regulate the cis-repressive RNA (crRNA) element that masks the ribosome binding site (RBS) of the transcript of particular gene through base pairing [4]. A well-known case named toehold switch has been applied on synthetic biology.

Recently, a CRISPR-Csy4 mediated activation method based on cis-repressive RNA cleavage has been achieved in bacteria [5]. This system significantly improved the feasibility of post-transcriptional regulation.

OUR INNOVATION AND ADVANTAGES

By reviewing existing methods and strategies, we are aware of some aspects worth optimizing. For general small RNA-mediated riboswitch, if the crRNA is perfectly paired with RBS, the trans-activating RNA will be hard to compete for the binding with crRNA. This may cause low activation efficiency for opening this type of switch. As for toehold switch, each switch needs to be individually designed. At the same time, introducing long homologous sequence for regulation may increase undesired recombination risks of foreign fragment insertion. [6].

This year, we designed and achieved a new alternative regulatory tool named "MiniToe Family", which is a new toolkit based on Csy4 produced by OUC-China.

Our journey

We have done

★We successfully registered our team for iGEM at February 8th.

★We met all deliverables on the Competition Deliverables page.

★We made a detailed description on what is done by ourselves and what is supported by others with precise attribution. Click here!

★We participated in the Interlab Measurement and submitted our result which was accepted by committee. Click here!

★We submitted 20 new Biobrick Parts designed by ourselves which play significant roles in our project and we sent 12 new Biobrick Parts among them. Click here!

★We have many kinds of collaborations related to our project! Foreign iGEM teams contacted us and helped us translate our comic book into 13 languages. More than 14 teams take our comic book——《E. coli SPACESHIP》to local areas for Science education. 4 team helped us test the function of our parts and we also helped them test their system. Three other teams and OUC-China formed the fundamental research results transformation group. We shared survey experience and formed a document, providing future iGEMers a reference. A new team was formed successfully with our help. Click here!

★We carefully confirmed that our work is safe and do not harm to the environment and society! Click here!

★We spread iGEM spirits and promoted the development of synthetic biology in China through popular science comic book——《E. coli SPACESHIP》! And we translated the book into several languages and spread it to many areas with the help of other iGEM teams! We also spread iGEM spirits by synthetic biology lecture, summer camp, and social media. Click here!

★We participated in synthetic biology forums —— Conference of China iGEMer Community (CCiC) as the co-organizer. Click here!

★We improved Part（BBa_K1062004）by point mutation and tested them by data support. They have functional improvement and both of them are the main roles of our system! The new parts we improved are BBa_K2615004, BBa_K2615005, BBa_K2615006, BBa_K2615007. See more details in this page! Click here!

★The models play an important role in our project and influenced our project deeply this year. For the first system, we built an ODE model and then the modeler helped us select mutants for second system. In miniToe polycistron, the model was also used to build a frame of whole structure. Click here!

★We successfully applied our system to the regulation of gene, motA! Click here!

reference

[1]. Glisovic T, Bachorik J L, Yong J, et al. RNA‐binding proteins and post‐transcriptional gene regulation[J]. Febs Letters, 2008, 582(14):1977-1986.

[2]. Bifulco P, Cesarelli M, Cerciello T, et al. Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells[J]. Current Opinion in Cell Biology, 2009, 21(3):452-460.

[3]. Lai E C. Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation.[J]. Nature Genetics, 2002, 30(4):363-364.

[4]. Karagiannis, P., Y. Fujita, and H. Saito.,RNA-based gene circuits for cell regulation. Proc Jpn Acad Ser B Phys Biol Sci, 2016. 92(9): p. 412-422.

[5]. Du, P., et al., Engineering Translational Activators with CRISPR-Cas System. ACS Synth Biol, 2016. 5(1): p. 74-80.

[6]. Green A, Silver P, Collins J, et al. Toehold switches: de-novo-designed regulators of gene expression.[J]. Cell, 2014, 159(4):925-939.