BIOCOMPLEXITY:ANALYSIS, DESIGN, EVOLUTION-COMPLEX GENES

生物复杂性：分析、设计、进化复杂基因

• 批准号: 6520550
• 负责人: Adam P Arkin
• 金额: $ 12.31万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-06-02 至 2004-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6520550
• 关键词: Escherichia coli; arabinose; biochemical evolution; bioengineering /biomedical engineering; biotechnology; cell type; chemoreceptors; computer simulation; experimental designs; gene expression; genetic promoter element; genetic regulation; mathematical model; pilin; quantitative trait loci; sensory mechanism

We propose the design and implementation of a protocol for the forward design of complex genetic circuitry for precise control of gene expression in a given cell type subject to a set of environmental or other cellular inputs. The ability to efficiently and accurately design and build such circuitry will facilitate a number of central biotechnological goals. For example, circuits might be designed to: 1) "instrument" cells to read out complex states, 2) maximize protein expression under different metabolic conditions, 3) perform a particular action (synthesis of a protein, initiation of a host-cell process) when particular conditions are met, or 4) provide a controllable mechanism by which a particular cellular system may be perturbed in a designed way to understand cellular function. Applications for such technology span the design of microorganisms for industrial protein production, to precise design of vectors for gene therapy. During the course of the project a theoretical and experimental framework to characterize naturally occurring genetic control circuits and to assemble novel genetic control circuits from the characterized parts to meet a particular control strategy will be developed. The specific aims may be concisely stated as: 1) to create and implement an experimental protocol designed to rapidly characterize and tune biological parts (promoters, terminators, transcripts, etc.) to sufficient detail that accurate mathematical models may be derived for the kinetics of each, 2) to create very detailed, experimentally validated models of cellular environmental sensing networks in which there are varying degrees of previous knowledge to hone the circuit analysis technology and provide conceptual models for future circuit designs; 3) using these results, to develop a streamlined protocol for computer-aided design of gene expression followed by implementation of a number of "canonical" circuit designs. As exemplars, we will study mathematically, computationally and experimentally, three "orthogonal" examples of genetic expression switches in E coli: the chemosensing arabinose promoter system, the type-1C pili phase variation control network, and the OmpR-mediated osmoregulatory system.

我们提出了一个复杂的遗传电路的正向设计的协议的设计和实施，精确控制基因表达在一个给定的细胞类型受一组环境或其他细胞输入。高效、准确地设计和构建此类电路的能力将促进许多核心生物技术目标的实现。例如，电路可以被设计为：1）“仪器”细胞读出复杂状态，2）在不同代谢条件下最大化蛋白质表达，3）执行特定动作（蛋白质的合成，宿主细胞过程的起始）当满足特定条件时，或4）提供一种可控机制，通过该机制，可以以设计的方式扰动特定的细胞系统，以理解细胞功能。这种技术的应用范围从工业蛋白质生产的微生物设计到基因治疗载体的精确设计。在该项目的过程中，将开发一个理论和实验框架，以表征自然发生的遗传控制电路，并从表征的部分组装新的遗传控制电路，以满足特定的控制策略。具体目标可以简明地表述为：1）创建和实施设计用于快速表征和调节生物部分（启动子、终止子、转录物等）的实验方案。2）创建非常详细的、实验验证的蜂窝环境感测网络的模型，其中存在不同程度的先前知识以磨练电路分析技术并为未来电路设计提供概念模型; 3）使用这些结果，开发用于基因表达的计算机辅助设计的流线型协议，随后实施许多“规范”电路设计。作为范例，我们将研究数学，计算和实验，在大肠杆菌中的基因表达开关的三个“正交”的例子：化学传感阿拉伯糖启动子系统，1C型皮利相位变化控制网络，和OmpR介导的转录调控系统。