Engineering biological complexity in yeast: synthetic pattern formation and emergence

增加生物复杂性的工程是生物设计工程的一个关键目标。理论研究已经揭示了简单的数学规则，这些规则在细胞群体的空间和时间模式中产生强大的异质性，可以被认为是“工程原理”。劳动分工和其他形式的异质性也是多细胞实体涌现特性的基础，通常在新陈代谢、运输、结构稳定性和反馈控制等重要功能上整体效率更高。合成生物学面临的一个雄心勃勃且及时的挑战是了解如何逆向工程并合理地设计对称性破坏事件以及随后在细胞群落中出现的紧急相互作用。这个跨学科的项目将开发合成生物学工具来预测设计和指导酵母的合成发育决策。为了控制多细胞的生长模式和形态发生，我们将使用合成基因调控来调节细胞分裂和生长的时间和频率，并指导细胞组之间的正交粘附。细胞将被编程为对细胞间通讯和侧向激活/抑制的反应进行分化。为了扩展模块化DNA资源，用于工程多细胞复杂性，本项目旨在创建一种用于自组织对称破断事件的新型分子机器。为了做到这一点，我们将从植物中转移一个具有良好特征的形态原系统，该系统提供了一个浓度依赖的分子开关。在植物中，生长素的积累协调了不同细胞的命运和生长调节。生长素在外排载体PIN蛋白的帮助下在细胞之间移动，PIN蛋白在细胞内显示极性定位。在酵母中，生长素已经是一种成熟的合成基因调控化学诱导剂。通过将PIN模块引入具有生长素调节基因控制的细胞，我们将能够编程酵母菌落内细胞间生长素流动和不对称浓度梯度。图像、视频和流式细胞术数据的数据分析，以及贝叶斯统计方法将用于生成参数，以填充细胞内基因回路的数学模型和描述不同细胞如何相互作用、通信和粘附的互补基于代理的模型。

Engineering increased biological complexity is a key goal for biodesign engineering. Theoretical studies have uncovered simple mathematical rules that generate robust heterogeneity in spatial and temporal patterns within cell populations that can be considered as 'engineering principles'. Division of labour and other forms of heterogeneity also underlie the emergent properties of a multicellular entity, often enabling higher efficiency as a whole in important functions like metabolism, transport, structural stability, and feedback control. An ambitious and timely challenge for synthetic biology is to understand how to reverse engineer and rationally design symmetry-breaking events and the emergent interactions that then follow in a community of cells.This interdisciplinary project will develop synthetic biology tools to predictively design and instruct synthetic developmental decision-making in yeast. To control multicellular growth pattern and morphogenesis, we will use synthetic gene regulation to modulate the timing and frequency of cell division and growth, and to instruct orthogonal adhesion between sets of cells. Cells will be programmed to differentiate in response to cell-to-cell communication and to lateral activation/inhibition. In order to expand the modular DNA resources for engineering multicellular complexity, this project aims to create a novel molecular machine for a self-organising symmetry-breaking events.To do this, we will transfer a well-characterised morphogen system from plants that provides a concentration-dependent molecular switch. In plants, accumulation of the hormone auxin coordinates differential cell fate and growth regulation. Auxin moves between cells with the aid of the efflux carrier PIN proteins, which show polar localisation within a cell. Auxin is already a well-established chemical inducer of synthetic gene regulation in the yeast. By introducing the PIN module into cells with auxin-regulated gene control, we will be able to program intercellular auxin flow and asymmetrical concentration gradient within a yeast colony. Data analysis of the images, videos, and flow cytometry data, along with Bayesian statistical methods will be used to generate parameters to populate mathematical models of the intracellular gene circuits and complementary agent-based models describing how the different cells interact, communicate and adhere.