Schultz - Proj 5

项目摘要 我们对抗生素耐药性的传统理解几乎完全基于细菌耐药性的概念。 种群在稳态药物条件下维持生长的能力。然而，它正变得越来越 显然，药物治疗的结果取决于高度动态的反应，需要复杂的 调控尽管越来越多的知识对监管电路的行为不同 类的抗肿瘤机制，定量了解这些架构如何演变 和多样性，以优化在不同环境中的表达仍然缺乏。全面了解 基因调控的设计原则是必不可少的，以解释如何控制机制可以减轻 抗生素耐药性的成本，并允许整个细菌种群的固定。最近的调查结果， 研究组的研究表明，大肠杆菌的四环素抗性、tet、操纵子等与大肠杆菌的四环素抗性有关。大肠杆菌，当突然暴露于 四环素通过快速表达外排泵（TetA）的阻遏物（TetR）来优化基因表达。 此外，基因表达的动态变化揭示了单细胞水平上细胞命运的多样性。 认识到细胞反应的时间依赖性成分对细胞免疫应答的产生有重要贡献， 生物体的适应性，这项研究的目标是调查进化优化的过程 在应对需要快速行动的环境压力时的抗生素反应（"动态功效"）。 本项目将以tet操纵子为重点，测试抗性基因调控的概念， 该机制针对基因表达的动力学进行了优化。通过以下具体目标， 研究将结合联合收割机生物信息学，数学建模和实验方法，以确定 各种优化的监管架构出现，以应对给定的环境约束， 解释基因调控如何多样化以应对生态挑战。拟议的目标是： 目标1.探索自然回路中抗生素反应的动力学：设计，最优性， 可变性这一目标将分析全基因组数据库，以调查自然变异将 确定有效耐药的关键调控策略。 目标2.开发针对特定动力学机制优化的合成电路。这方面的工作将 开发抗生素耐药性的定量模型，以设计和实施最佳监管架构 并研究自然界中发现的基因调节是针对特定环境优化的假设。 目标3：在不同的药物方案中进行耐药机制的实验演变。这 aim将在不同的动力学设置下实验性地进化出一种抗性机制，以探索基因是如何 法规变化以应对新的环境挑战。 了解基因调控的变化如何定义细胞过程的动力学， 直接告知新的抗菌治疗的发展，并解释如何失调可能是 人类疾病的原因，如癌症。 !

PROJECT SUMMARY Our conventional understanding of antibiotic resistance is based almost entirely on the notion of a bacterial population’s ability to maintain growth under steady-state drug conditions. Yet, it is becoming increasingly apparent that the outcome of drug treatment depends on highly-dynamic responses that require complex regulation. Despite a growing body of knowledge on the regulatory circuits governing the behavior of different classes of antibiotic-resistance mechanisms, a quantitative understanding of how these architectures evolved and diversified to optimize expression in different environments is still lacking. A comprehensive understanding of the design principles of gene regulation is essential to explain how control mechanisms can mitigate the costs of antibiotic resistance and allow fixation throughout bacterial populations. Recent findings from this research group show that the tetracycline resistance, tet, operon in E. coli, when suddenly exposed to tetracycline, optimizes gene expression by rapidly expressing the repressor (TetR) of the efflux pump (TetA). Moreover, variations in the dynamics of gene expression reveal a diversity of cell fates at the single-cell level. Recognizing that the time-dependent component of cell responses makes an important contribution to the fitness of an organism, the goal of this study is to investigate the process by which evolution optimizes antibiotic responses when addressing environmental pressures that require fast action (“dynamical efficacy”). Focusing on the tet operon, this project will test the concept that gene regulation of a resistance mechanism is optimized for the dynamics of gene expression. Through the following specific aims, this study will combine bioinformatics, mathematical modeling, and experimental approaches to determine what kinds of optimized regulatory architectures emerge in response to given environmental constrains, and to explain how gene regulation can be diversified in response to ecological challenges. The proposed aims are: Aim 1. Explore the dynamics of antibiotic response in natural circuits: design, optimality, and variability. This aim will analyze whole-genome databases to investigate the idea that natural variation will identify key regulatory strategies for effective resistance. Aim 2. Develop synthetic circuits optimized for specific dynamical regimes. Work in this aim will develop quantitative models of antibiotic resistance to design and implement optimal regulatory architectures and investigate the hypothesis that gene regulation found in nature is optimized to specific environments. Aim 3. Perform experimental evolution of resistance mechanisms in different drug regimes. This aim will experimentally evolve a resistance mechanism under different dynamical settings to explore how gene regulation changes in response to new environmental challenges. The understanding of how changes in gene regulation define the dynamics of cellular processes will directly inform the development of new antimicrobial therapies and explain how misregulation may be the cause of human disease, such as cancer. !