細菌極化和不對稱分裂之多個體計算模型

An individual-based computational model for polarization and asymmetric cell division in Escherichia coli

潘政儒(Cheng-Ju Pan)

指導教授 ： 黃筱鈞

國立臺灣大學/生命科學院/分子與細胞生物學研究所/碩士(2015年)

https://doi.org/10.6342/NTU.2015.11227

摘要

在合成生物學當中有一種新的基因線路可以在對稱分裂的大腸桿菌中使之表現PopZ蛋白，並產生蛋白極化和細胞不對稱分裂的現象。但是在這個合成生物系統當中，確切的細胞行為以及產生蛋白質極化的原理仍有許多尚未被理解的部分。在合成生物學的研究當中，常常會透過數學模型來分析系統當中關鍵的參數以及最佳化實驗設計。在這篇論文裡，我提出一個多個體的計算模型：這種模型可以用來模擬非同源表現PopZ蛋白的大腸桿菌。模型主要的目的是去描述PopZ透過與同類分子交互作用聚合的現象，以及PopZ是否會形成更高級的結構，並在細胞中產生極化的狀態。論文中會討論模型裡，哪些分子交互作用的規則能夠促使產生穩定而不易崩潰的單極化細胞。模型首先再現了實驗中隨著PopZ表現量差異因而造成細胞極化狀況不同的現象，接著我們在模型裡加入另一個已知會與PopZ交互作用的非同源膜蛋白SpmX，來探討相關的行為。模型再一次重現了實驗中SpmX促進PopZ在細胞當中極化的趨勢。除此之外將模型從二維延展至三維展示了模型的規則同樣適用於更貼近真實細胞生理的狀態。最後，模型導入細胞分裂的現象，相關的模擬結果提供了關於PopZ聚集的焦點是如何被細胞繼承下去，並產生不對稱分裂的現象。這個多個體計算模型提供了一個可以透過電腦模擬來研究PopZ於大腸桿菌中極化的平台。

關鍵字

蛋白極化 ； 不對稱分裂 ； 多個體計算模型 ； 合成生物學 ； 電腦模擬

並列摘要

Engineered PopZ polarization and asymmetric cell division in a symmetrically dividing Escherichia coli cell is a novel genetic circuit construction in synthetic biology. Cellular behavior and underlying principles of protein polarization are not well understood in this synthetic system. Mathematical modeling, which is broadly applied in systems of synthetic biology, may help researchers to analyze critical parameters and to optimize experimental design. In this thesis, I introduced an individual-based computational model for simulation of Escherichia coli heterologously expressing PopZ protein. The model described the oligomerization of PopZ proteins with molecular interactions, and whether PopZ forms higher order structures dictating the polarization states of a cell. I discussed molecular interacting rules in the model that lead to robust PopZ unipolarization. Our model first recapitulated the polarization of cell over differential level of PopZ expression. Then another heterologous membrane protein SpmX, which is known to interact with PopZ, was introduced into the system. Our model also recapitulated a trend similar to our experimental data, which is the interaction of PopZ with SpmX promotes PopZ polarization in a cell. Extension of our model from 2-dimension to 3-dimension demonstrated that the rules in our system can be adapted to a more physiological relevant cell state. Finally, we implemented cell division in the model, and the result provided some intuition for how PopZ foci may be inherited in engineered asymmetric cell division. This individual-based model provides a platform to study PopZ polarization in Escherichia coli in silico.

並列關鍵字

Protein polarization ； Asymmetric cell division ； Individual-based modeling ； Synthetic biology ； Computer simulation

參考文獻

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