Modeling and Analysis of Bacterial Signaling Circuits

描述（由申请人提供）：双组分系统是细菌信号转导的主要模式之一。通过数学建模和实验，它们为探索细胞信号传导的许多基本设计原理提供了一种优秀的电路。这项研究的长期目标是开发和测试大肠杆菌双组分系统网络的数学模型。本提案中的研究将建立在先前工作的基础上，我们已经为一些最简单的双组分信号示例制定了数学模型，并开发了一些新的实验工具来研究这些系统。这项研究将结合数学模型和实验测试，利用遗传学和荧光显微镜来跟踪活细胞信号传递过程的各个步骤。本课题的具体目的是：1)分析双组分信号磷酸化周期的动力学和稳态下电路的特性；2)分析正自调节在双组份信号中的作用，确定其对电路稳态和动态特性的影响，并使用PhoQ/PhoP双组份系统测试预测结果；3)建立和测试体内应答调节因子与DNA结合的模型，推断结合应答调节因子的比例与转录活性之间的功能关系；4)开发和测试来自单独的双组分系统和其他供磷体的弱串扰模型，以验证调节蛋白的磷酸化周期和化学计量对串扰抑制很重要的假设。许多双组分信号系统在发病机制中起重要作用。这些包括调节毒力决定因子表达的回路，以及病原体生存所必需的更一般的应激反应或抗生素抗性系统。提高对这些电路结构的理解和有用的模型来理解电路扰动的影响，可能有助于我们对病原体的毒力和生存的理解，并有助于开发新的抗菌剂。

DESCRIPTION (provided by applicant): Two-component systems are one of the major modes of signal transduction in bacteria. They provide an excellent class of circuits for exploring, through mathematical modeling and experiments, many of the basic design principles underlying cell signaling. The long-term objectives of the research in this proposal are to develop and test mathematical models for the network of two-component systems in E. coli. The research in this proposal will build on previous work in which we have formulated a mathematical model for some of the simplest examples of two-component signaling and have developed a number of new experimental tools for studying these systems. The research will combine mathematical modeling with experimental tests that make use of genetics and fluorescence microscopy to follow various steps in the signaling process in live cells. The specific aims of this proposal are to: 1) Analyze the dynamics of the phosphorylation cycle in two- component signaling and properties of the circuit at steady state; 2) Analyze the role of positive autoregulation in two-component signaling to determine its effects on the steady-state and dynamic properties of the circuit and test the predictions using the PhoQ/PhoP two-component system; 3) Develop and test models for response regulator binding to DNA in vivo to infer the functional relation between the fraction of bound response regulator and transcriptional activity; 4) Develop and test a model of weak crosstalk from a separate two-component system and from other phosphodonors to test the hypothesis that the phosphorylation cycle and stoichiometry of regulatory proteins are important for crosstalk suppression. Many two-component signaling systems play important roles in pathogenesis. These include circuits that regulate the expression of virulence determinants as well as more general stress-responsive or antibiotic resistance systems that are necessary for the survival of pathogens. An improved understanding of the structure of these circuits and useful models to understand the effects of circuit perturbations will likely contribute to our understanding of virulence and survival of pathogens and aid in the development of novel antimicrobials.