RoL: FELS: RAISE: Balancing demands of Minimal Cell

建立细胞生命的核心要求和原理是生物学和生物物理学的基本挑战。该项目解决了细胞生长和复制所必需的最小生化功能的生命规则问题。该项目特别涉及最小细胞的简化代谢模型的开发。这项工作的主要贡献是理解在给定的约束环境中，基本代谢过程与细胞过程之间能量交换的大规模经济之间的相互作用。该模型揭示了在细胞周期的时间尺度上，细菌菌落生长所必需的细胞事件之间的最小化学相互作用过程。虽然这个模型是为最简单的活细胞推导出来的，但它包含了所有形式的细胞生命所必需的过程，因此产生了适用于整个细胞生命的见解。该模型的简洁性使得广大的研究人员和非科学家更容易理解细胞生命的原理。圣地亚哥地区的本科生通过与J. Craig Venter研究所的安排参与该项目。根据这种安排，学生进行必要的实验室工作，使用基因编辑遗传工具来消除工程细菌细胞中连接代谢网络的基因。该项目涉及使用模型系统JCVI-syn3A，这是一种最小的细菌细胞，是与J. Craig Venter研究所的合成生物学小组共同开发的。该方法采用自下而上的设计方法。该模型显示了代谢子系统之间高度降低的耦合。进一步简化JCVI-syn3A产生一个细胞系统，其中基本过程不仅定义良好，而且几乎是孤立的。这些环境为研究生命的基础以及特定的细胞行为是如何从个体过程的输出中产生的提供了基础。计划在具有代表性的代谢物和营养物质、代谢酶、转运蛋白、遗传信息加工蛋白、DNA和RNA水平上构建粗粒度的JCVI-syn3A半分析动力学模型。在单细胞分辨率下进行单分子实验，量化JCVI-syn3A中标记转运蛋白的数量，以改变模型的初始条件。该动力学模型用于指导通过遗传修饰验证的代谢子系统之间耦合的最小化。该项目由分子和细胞生物科学部的系统和合成生物学集群以及物理部的生命系统物理学项目共同资助。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Establishing the core requirements and principles of cellular life is a fundamental challenge of biology and biological physics. This project addresses the Rules of Life question of the minimum biochemical functions that are necessary for a cell to grow and replicate. The project specifically involves the development of a simplified metabolic model for a minimal cell. The major contribution of this work is understanding interactions between the fundamental metabolic processes and large-scale economy of energy exchange among cellular processes in a given constrained environment. This model reveals the minimal chemical interacting processes between cellular events necessary for the growth of bacterial colonies over the time scale of cell cycles. While being derived for the simplest viable cell, this model encompasses processes essential to all forms of cellular life and hence yields insights applicable to cellular life as a whole. The simplicity of the developed model makes the principles of cellular life more accessible to a broad audience of researchers and non-scientists. Undergraduate students in the San Diego area are involved in the project through an arrangement with the J. Craig Venter Institute. According to this arrangement students perform essential lab work to use gene editing genetic tools to eliminate genes linking the metabolic networks in engineered bacterial cells.The project involves use of the model system JCVI-syn3A, a minimal bacterial cell that was developed in conjunction with the Synthetic Biology group at the J. Craig Venter Institute. The approach used a bottom-up design method. This model displayed a highly reduced coupling between metabolic subsystems. Further simplification of JCVI-syn3A yields a cellular system where fundamental processes are not only well defined but also nearly isolated. These circumstances provide the foundation to study the basics of life and how specific cellular behaviors emerge from the output of individual processes. The plan is to construct a semi-analytical kinetic model of JCVI-syn3A coarse-grained at the level of representative metabolites and nutrients, metabolic enzymes, transporter proteins, genetic information processing proteins, DNA and RNA. Single-molecule experiments at single-cell resolution are performed to quantify the number of labeled transporter proteins in JCVI-syn3A to vary initial conditions for the models. The kinetic model is used to guide the minimization of the coupling between the metabolic subsystems which are validated through genetic modifications.This project is co-funded by the Systems and Synthetic Biology cluster in the Division of Molecular and Cellular Biosciences and the Physics of Living Systems program in the Division of Physics.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.