Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies
Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies
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DOI：
10.1021/acssynbio.6b00149
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发表时间：
2017-02-01
影响因子：
4.7
通讯作者：
Federici, Fernan
中科院分区：
文献类型：
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作者：
Nunez, Isaac N.;Matute, Tamara F.;Federici, Fernan
形态发生工程是一个新兴领域，探索由细胞和群体机器人等多个主体组成的系统中自组织模式、形态和架构的设计和实现。另一方面，合成生物学旨在开发工具和形式主义，以提高生物系统工程的可重复性、易处理性和效率。我们寻求将合成生物学方法应用于多细胞系统的形态工程。在这里，我们描述了两种机制的工程，对称性破坏和域特异性细胞调节，作为细菌菌落形态发生指令原型设计的基本功能。前者代表基于质粒分离的人工图案化机制，而后者通过普遍存在的和分离的成分的空间共定位来发挥人工细胞分化的作用。这种图案化与驱动的分离促进了设计-构建-测试-改进工程周期。我们为 CellModeller 创建了代表这些基本功能的计算模块，并用它来指导设计过程并在计算机中探索设计空间。我们应用这些工具来编码空间结构功能，例如代谢互补、RNAPT7 基因表达和 CRISPRi/Cas9 调控。最后，作为概念验证，我们使用 CRISPRi/Cas 技术通过控制蛋氨酸合成来调节细胞生长。这些机制从单细胞开始，使得能够自下而上地研究形态发生原理和新型群体规模结构的工程。
Morphogenetic engineering is an emerging field that explores the design and implementation of self-organized patterns, inorphologies, and architectures in systems composed of multiple agents such as cells and swarm robots. Synthetic biology, on the other hand, aims to develop tools and formalisms that increase reproducibility, tractability, and efficiency in the engineering of biological systems. We seek to apply synthetic biology approaches to the engineering of morphologies in multicellular systems. Here, we describe the engineering of two mechanisms, symmetry-breaking and domain-specific cell regulation, as elementary functions for the prototyping of morphogenetic instructions in bacterial colonies. The former represents an artificial patterning mechanism based on plasmid segregation while the latter plays the role of artificial cell differentiation by spatial colocalization of ubiquitous and Segregated components. This separation of patterning from actuation facilitates the design-build-test-improve engineering cycle. We created computational modules for CellModeller representing these basic functions and used it to guide the design process and explore the design space in silico. We applied these tools to encode spatially structured functions such as metabolic complementation, RNAPT7 gene expression, and CRISPRi/Cas9 regulation. Finally, as a proof of concept, we used CRISPRi/Cas technology to regulate cell growth by controlling methionine synthesis. These mechanisms start from single cells enabling the study of morphogenetic principles and the engineering of novel population scale structures from the bottom up.