Team:OUC-China
In this project, dry experiments are strongly linked to wet experiments. First, systems biology modeling is utilized to verify that the plasmid copy number can be controlled by replacing weak promoters while increasing the copy number and simulated components in quorum sensing system. Besides it is successful to simulate the system of RNA transporter, riboswitch and hardware to provide data support for subsequent experiment. After successful validation of quorum sensing, structure and function of the protein in Aureobasidium melanogenum P16 that has the same function as AtLPT4 protein in Arabidopsis are analyzed. Utilizing the principle ‘design RNA aptamers in silico’, aptamers that can interact with the ligand GABA are successfully designed in silico by docking and molecular dynamic, RNA transporter and riboswitches are constructed by analyzing the secondary and tertiary structures of them. Simulate the survival and yield of engineering bacteria in the fermentation tank by the idea of cellular automata. Finally, utilizing machine learning algorithms, combined with transcriptome data, promoter is designed in silico to add components for the new type of fermentation chassis.
Overview
Systems biology modeling
Systems modeling is built to simulate the weak promoter system to verify the viability of our idea to replace the PFK promoter with a weak expressed promoter to maintain the copy number of the plasmid. Beside to make our quorum sensing system better adapted to different fermentation environments, emulation techniques is utilized to simulate the performance of different SSRE promoters to provide data support for subsequent wet experiments. What’s more, due to the time, the system of transport RNA, riboswitch, and hardware with different performance can only be simulated to visualize its results and it provide theories to change the components to achieve the perfect effect.
Design aptamers in silico and structural analysis
It this part, aptamer that can specifically bind to GABA is designed in silico, and verified its performance by docking analysis and molecular dynamic(MD). RNA transporter and riboswitch are retrofitted by the aptamer. Besides new aptamer is redesigned as the result from wet experiment is not ideal, the newly built aptamer is much better than the one above.
Cellular automata simulation analysis
As the time limits, there is no time to verify the entire system, so the idea of cellular automata is utilized to simulate the fermentation of CHIP and ordinary engineering bacteria to prove the superiority of CHIP.
Protein structure analysis
As the validation in wet experiments, it is concluded that the AtPT4 protein must be presented in Aureobasidium melanogenum P16. Sequences align is utilized to search the similar sequence in Aureobasidium melanogenum P16 genome. Besides docking analysis and molecular dynamics are utilized to analyze them.
Design promoter in silico
As Aureobasidium melanogenum P16 is new frmentation chassis organism, it is yet developed. Therefore, machine leaning is utilized to design a promoter with expected performance with two model. The first model is to generate the sequence of a promoter, another is to predict the expression strength of the promoter.
Summary
This dry experiment focused on simulating and adding new components for the engineering bacteria. As the time is limited, the designed components cannot be tested in wet experiment, so utilizing the simulation method, not only can visualize the effect of the components, but also simulate the differences of different components, provide data support for the subsequent wet experiment. This is also the idea advocated by synthetic biology nowadays.
