Systems Biology of Sporulation in Bacillus Subtilis

描述(申请人提供)：本提案旨在将数学和统计学的方法应用于理解枯草杆菌芽胞形成的实验系统中的发育基因控制。对于这种跨学科的方法来说，这是一个理想的系统，因为孢子形成是一个相对原始的发育系统，非常容易获得遗传学、生物化学和细胞学的工具。具体目标是了解孢子形成途径中的三个关键DNA结合蛋白(主调节蛋白)是如何识别它们的靶标的，并对控制孢子形成基因表达程序启动的电路进行建模。将设计和进行生化和分子遗传学实验，以探索负责蛋白质结合的DNA序列特征，以满足计算策略的发展。反过来，将对计算预测进行实验测试，以提供反馈以改进计算模型。还将开发模型，以了解基因如何对关键主调控子SpoOA的浓度做出不同的反应，并解释SpoOA的缓慢积累如何以及为什么在孢子形成启动中发挥关键作用。 孢子形成的综合优点是，在一个非常适合定量方法的系统中代表一个重大的生物学问题。因此，在设计定量方法来描述孢子形成系统的分子成分之间的相互作用方面取得的进展应该作为更复杂的生物系统的计算方法的模型。这项建议的一个显著特点是，理论工作将与实验齐头并进，以便通过快速的经验反馈提供定量建模的信息，反过来，数学模型可以指导实验的设计和数据收集，还可以提出对某些分析最有帮助、对现有数据最具互补性的数据类型。 这项研究将有助于更大的系统生物学领域，该领域试图定量地描述“根据分子成分的复杂生物组织和过程的行为”(Mark Kirschner)。这项拟议的研究与人类健康相关，因为疾病通常涉及对细胞调节组件之间相互作用的复杂网络的扰动，并将适用于设计定量方法来理解正常和异常细胞状态下的生物组织。对枯草杆菌产孢量的透彻了解还可以为打击生物恐怖主义和由类似细菌引起的疾病提供知识，如炭疽杆菌。

DESCRIPTION (provided by applicant): This proposal aims to bring the methods of mathematics and statistics to bear on understanding developmental gene control in the experimental system of sporulation in the bacterium Bacillus subtilis. This is an ideal system for such an interdisciplinary approach because sporulation is a relatively primitive developmental system and is highly accessible to the tools of genetics, biochemistry and cytology. The specific goals are to understand how three key DNA-binding proteins (master regulators) in the sporulation pathways recognize their targets, and to model the circuitry that governs the initiation of the program of sporulation gene expression. Biochemical and molecular genetic experiments will be designed and conducted to probe DNA sequence features responsible for protein binding so as to feed to the development of computational strategies. In turn computational predictions will be tested experimentally to provide feedbacks to improve computational models. Models will also be developed to understand how genes respond differently to the concentration of a key master regulator SpoOA, and to explain how and why the slow accumulation of SpoOA plays a key role in the sporulation initiation. Sporulation has the combined virtues of representing a significant biological problem in a system that is well suited to quantitative approaches. Hence, the progress made here in devising quantitative methods to describe the interactions among the molecular constituents of the sporulation system should serve as a model for computational approaches to more complicated biological systems. A distinctive feature of this proposal is that the theoretical work will be carried out hand-in-hand with experimentation so that quantitative modeling can be informed by rapid empirical feedback and, conversely, mathematical models can guide the design of experiments and data collection, and can also suggest the types of data that are most helpful for certain analyses and most complementary to existing data. The research will contribute to the larger field of systems biology, which attempts to describe quantitatively "the behavior of complex biological organization and processes in terms of the molecular constituents" (Mark Kirschner). The proposed research is relevant to human health because disease typically involves perturbations to the complex web of interactions among cellular regulatory components and will be applicable to devising quantitative approaches to understanding biological organization in normal and abnormal cellular states. A thorough understanding of B. subtilis sporulation can also provide knowledge for combating bio-terrorism and diseases that are caused by similar bacteria, such as Bacillus anthracis.