Using a queueing framework to explore the design principles of synthetic circuits in microorganisms

在资源（如营养物质）有限的环境中生存是各种微生物系统面临的挑战。尽管长期以来人们一直认识到微生物适应和进化以应对资源限制，但仍然需要更好地了解参与有限资源处理的细胞机制在细胞中是如何重要的，包括控制蛋白质生产，降解和修饰的分子机器。研究小组探索了大肠杆菌中控制合成和天然生物“电路”的基本设计原则，这些设计原则是细胞资源分配过程的核心。除了描述资源处理和分配机制外，该项目还开发了一个相关的排队理论（等待队列的数学研究）框架来分析该系统，这将为生物分子资源分配系统提供一个统一和直观的框架。作为该项目的教育广泛影响的一部分，研究人员将招募学生，包括那些来自代表性不足的群体的学生，参加合成生物学研究经验。此外，该项目将为K-12科学教师提供专业发展讲习班，以提高他们将合成生物学模块融入课堂的能力。细胞机制涉及代谢、转录、翻译和蛋白质降解等关键过程，其设计目的是在资源有限时避免细胞系统超载，因为超载可能导致排队等候（即生物排队）的形成。为了研究生物分子过程中的排队，本项目将荧光显微镜和微流体等技术与合成生物学和定量建模相结合，以推断合成和天然生物网络动力学背后的理论排队原则。专注于大肠杆菌细胞的蛋白水解途径，研究人员将单细胞和高通量技术结合起来，量化和数学模型的串扰，或蛋白水解瓶颈，目标蛋白和竞争多种降解途径。该项目的结果有可能推进排队理论在合成电路分析中的应用，并增强我们对原生生物过程如何分配动态变化资源的理解。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。

Survival in environments with limited resources (e.g. nutrients) is a challenge encountered by a variety of microbial systems. Although it has long been appreciated that microbes adapt and evolve to cope with resource limitations, there remains a need to better understand how cellular machinery involved in the processing of finite resources are important in a cell, including molecular machines that control protein production, degradation, and modification. The team of investigators explores the underlying design principles governing synthetic and native biological "circuits" in E. coli that are central to cellular resource allocation processes. In addition to characterizing the resource processing and allocation machinery, the project develops an associated queueing theory (a mathematical study of waiting lines) framework to analyze the system, which will provide a unifying and intuitive framework for biomolecular resource allocation systems. As part of the educational Broader Impacts of the project, investigators will recruit students, including those from underrepresented groups, to participate in synthetic biology research experiences. Additionally, the project will provide professional development workshops for K-12 science teachers to enhance their ability to integrate synthetic biology modules into their classrooms. The cellular machinery involved in crucial processes such as metabolism, transcription, translation, and protein degradation are designed to avoid overloading cellular systems when resources are limited, as overloading could lead to the formation of waiting lines (i.e., biological queueing). To investigate queueing in biomolecular processes, this project combines techniques, such as fluorescence microscopy and microfluidics, with synthetic biology and quantitative modeling to infer theoretical queueing principles behind the dynamics of both synthetic and native biological networks. Focusing on proteolytic pathways in E. coli cells, investigators combine single-cell and high-throughput techniques to quantify and mathematically model crosstalk, or proteolytic bottlenecks, between proteins targeted to and competing for multiple degradation pathways. Results of this project has the potential to advance the use of queueing theory for the analysis of synthetic circuits and enhance our understanding of how native biological processes allocate dynamically varying resources.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.