Modeling and Analysis of Bacterial Signaling Circuits

描述(申请人提供)：双组分系统是细菌信号转导的主要模式之一。它们提供了一类极好的电路，可以通过数学建模和实验探索细胞信号的许多基本设计原则。这项研究的长期目标是开发和测试大肠杆菌中双组分系统网络的数学模型。这项建议中的研究将建立在以前的工作的基础上，在这些工作中，我们已经为一些最简单的两分量信令示例建立了数学模型，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建模和实验测试，利用遗传学和荧光显微镜来跟踪活细胞中信号传递过程的不同步骤。这一建议的具体目的是：1)分析双组分信号中磷酸化循环的动力学和稳态下电路的性质；2)分析正自动调节在双组分信号中的作用，以确定其对电路的稳态和动态特性的影响，并使用PhoQ/Phop双组分系统验证预测；3)建立和测试体内与DNA结合的反应调节器模型，以推断结合反应调节器比例与转录活性之间的函数关系；4)从一个单独的双组分系统和其他磷酸盐系统建立并测试弱串扰模型，以验证调节蛋白的磷酸化周期和化学计量比对串扰抑制重要的假设。许多双组分信号系统在发病机制中发挥着重要作用。其中包括调节毒力决定因素表达的回路，以及病原体生存所必需的更一般的应激反应或抗生素耐药系统。更好地了解这些电路的结构和有用的模型来了解电路扰动的影响，可能有助于我们了解病原体的毒力和生存，并有助于开发新型抗菌剂。

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.