Nuñez Isaac N, Matute Tamara F, Del Valle Ilenne D, Kan Anton, Choksi Atri, Endy Drew, Haseloff Jim, Rudge Timothy J, Federici Fernan
Escuela de Ingeniería, Pontificia Universidad Católica de Chile , 7820436, Santiago, Chile.
Fondo de Desarrollo de Areas Prioritarias Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile , 7820436, Santiago, Chile.
ACS Synth Biol. 2017 Feb 17;6(2):256-265. doi: 10.1021/acssynbio.6b00149. Epub 2016 Nov 28.
Morphogenetic engineering is an emerging field that explores the design and implementation of self-organized patterns, morphologies, 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.
形态发生工程是一个新兴领域，它探索在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、形态和架构的设计与实现。另一方面，合成生物学旨在开发工具和形式体系，以提高生物系统工程中的可重复性、可操作性和效率。我们试图将合成生物学方法应用于多细胞系统形态的工程设计。在此，我们描述了两种机制的工程设计，即对称性破缺和特定区域细胞调控，作为细菌菌落中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和分离的成分在空间上的共定位起到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 - 改进的工程循环。我们为CellModeller创建了代表这些基本功能的计算模块，并利用它来指导设计过程并在计算机上探索设计空间。我们应用这些工具来编码空间结构化功能，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技术通过控制甲硫氨酸合成来调节细胞生长。这些机制从单细胞开始，能够自下而上地研究形态发生原理并设计新型群体规模结构。
