Assessment of Pathway Design Through Multi-level Modeling and Experimentation

这项研究的长期目标是发现和理解生物网络的设计和运作原理。作为实现这一目标的第一步，该项目对一个小系统进行了非常详细的多层次分析，即酵母中的海藻糖循环。这个系统代表了许多途径系统，因为生物学通常是模块化和分层的，从这个小系统中获得的见解对于合理化其他更大的系统至关重要。海藻糖是一种双糖，它为微生物提供了一种重要的防御机制，可以抵御各种各样的压力，包括高温、静水压力、干燥、营养饥饿、渗透或氧化应激以及暴露于有毒化学物质。在压力酵母中，海藻糖以惊人的速度和大量产生。一旦压力停止，海藻糖就会迅速循环为葡萄糖。这种应激反应系统非常有趣，因为它使细胞面临复杂的任务，即以最有效和最适合当前环境条件的方式引导物质进行糖酵解、糖原储存或海藻糖生产。细胞通过一个复杂的代谢和基因组控制网络来管理这个三方决定，该网络围绕着该途径的关键代谢分支点，葡萄糖6-磷酸。尽管已经对应激细胞中海藻糖循环的许多特性进行了广泛的研究，但这种高度调节系统的动力学还没有得到很好的理解。事实上，这个周期显示出违反直觉的、迄今为止无法解释的特征，比如在海藻糖需求最大的时候，编码海藻糖降解酶的基因的强烈上调。该项目通过对所有相关基因的表达、所有相关酶的活性和所有相关代谢物的密集时间序列测量，阐明了海藻糖系统的功能。这些数据将为综合分析提供前所未有的机会，其中将包括新的统计和系统生物学方法。除了加深对这一特定系统的理解之外，该项目还将成为理解综合和高度调节的代谢途径系统的多学科方法的范例。更广泛的影响该项目中实验和数值分析的结合为研究生和博士后创造了一个优秀的训练基地，他们将熟悉21世纪系统导向生物学中必不可少的一系列工具。学员将学习如何从文献中提取各种生物信息和分析技术，发明新技术，并将数据和方法锻造成跨学科的工具，以解决他们以前没有遇到过的问题。

The long-term goal of this research is to discover and understand design and operating principles of biological networks. As a first step toward this goal, the project investigates a very detailed, multi-level analysis of a small system, namely the trehalose cycle in yeast. This system is representative for many pathway systems, and because biology is often modular and hierarchical, insights gained from this small system will be crucial for rationalizing other and larger systems. Trehalose is a disaccharide that equips microorganisms with an important defense mechanism against a wide variety of stresses, including high temperature, hydrostatic pressure, desiccation, nutrient starvation, osmotic or oxidative stress, and exposure to toxic chemicals. In stressed yeast, trehalose is produced with amazing speed and in enormous quantities. Once the stress ceases, trehalose is quickly recycled to glucose. This stress response system is very interesting because it confronts the cell with the complex task of channeling material toward glycolysis, glycogen storage, or trehalose production in a manner that is efficient and most appropriate for its present environmental conditions. The cell manages this three-way decision through an intricate network of metabolic and genomic controls surrounding the critical metabolic branch point of the pathway, glucose 6-phosphate. Even though many specific properties of the trehalose cycle in stressed cells have been studied extensively, the dynamics of this highly regulated system is not well understood. Indeed, the cycle exhibits counterintuitive and so far unexplained features, such as the strong up-regulation of genes that code for trehalose-degrading enzymes at the time of greatest trehalose demand. This project elucidates the functioning of the trehalose system through dense time series measurements of the expression of all relevant genes, of the activities of all relevant enzymes, and of all pertinent metabolites. The data will provide an unprecedented opportunity for integrative analysis, which will include novel statistical and systems biological methods. Beyond yielding deeper understanding of this particular system, this project will serve as a paradigm for multi-disciplinary approaches to understanding integrated and highly regulated metabolic pathway systems. Broader ImpactsThe merging of experimental and numerical analyses within this project creates an outstanding training ground for graduate students and postdoctoral fellows, who will gain intimate familiarity with a repertoire of tools that are becoming mandatory in the systems-oriented biology of the 21st Century. The trainees will learn how to extract diverse biological information and analytical techniques from the literature, invent new techniques, and to forge data and methods into interdisciplinary tools for addressing issue they have not encountered before.