Probing Metabolic Complexity Using a Bacterial Model System

使用细菌模型系统探测代谢复杂性

• 批准号: 7221021
• 负责人: Jeff M Boyd
• 金额: $ 4.68万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-02-01 至 2009-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7221021
• 关键词: ATP phosphohydrolase; Address; Anabolism; Area; Bacterial Model; Binding; Biochemical; Biochemical Process; Biological Assay; Biological Models; Biology; Cell physiology; Cells; Disease; Excision; Face; Free Radicals; Genetic; Genome; Goals; Homeostasis; In Vitro; Internet; Iron; Knowledge; Life; Malignant Neoplasms; Metabolic; Metabolic Pathway; Metabolism; Metals; Nutrient; Open Reading Frames; Organism; Physiological; Physiology; Proteins; Refractory; Research; Role; Salmonella enterica; Series; Starvation; Sulfur; Sum; System; Techniques; Testing; Thiamine; Time; Training; Vitamin, Other; Work; base; career; chemical reaction; genetic analysis; genome sequencing; in vitro Assay; in vivo; repaired; research study; trafficking

DESCRIPTION (provided by applicant): A fundamental question in biology is how the integration of metabolic pathways is regulated to produce the robust, but responsive physiology that characterizes sustainable life. Our lack of basic knowledge in these areas is emphasized by the multiple ORFs that remain without functional annotation in diverse genome sequences. Because all living cells face similar challenges in integrating their metabolism, a bacterial system (Salmonella enterica) will be used for simplicity and technical feasibility to complete the outlined objectives. This system will provide training in dissecting a network that can be transferred to more refractory organisms later in my career. Genetic analysis of the system integrated with thiamine biosynthesis has identified a set of five conditional thiamine axotrophs which are defective in Fe-S cluster metabolism. Collectively, these loci appear to be necessary for Fe trafficking, and the repair of oxidatively damaged Fe-S clusters. A series of experiments is outlined to address the specific biochemical function of three of these proteins (ApbE, ApbC, and RseC). The project described herein is divided into two similar and overlapping objectives that will ultimately define the relationship between these and other proteins involved in Fe-S metabolism. Completion of these objectives will require in vivo and in vitro experiments with rigorous application of biochemical, biophysical, genetic, and physiological techniques. The long-term goal of the research presented in this proposal is to contribute to the understanding of metabolic integration, specifically Fe homeostasis. To reach this goal we must increase our knowledge of the biochemical components of metabolism and the connections that exist between them. Such work not only contributes to the rigorous annotation of genomes, but provides the basis for continuing studies on Fe and free radical metabolism. Cellular metabolism is the sum of all of the chemical reactions taking place in a living cell at any given time. Like the internet or the economy, metabolism is a network or system, so small changes, such as the removal of a nutrient, can have profound effects. The objective of the proposed work is to understand the connections between these chemical reactions in order to predict the effects which would be encountered if the system is in some way perturbed (cancer, starvation, disease etc.).

描述（由申请人提供）：生物学中的一个基本问题是如何调节代谢途径的整合，以产生以可持续生命为特征的稳健但响应性的生理学。我们缺乏这些领域的基本知识，强调了在不同的基因组序列中仍然没有功能注释的多个ORF。由于所有活细胞在整合其代谢方面都面临类似的挑战，因此为了简单和技术可行性，将使用细菌系统（沙门氏菌）来完成所概述的目标。这个系统将提供解剖网络的培训，在我的职业生涯后期，这种网络可以转移到更难处理的生物体上。整合硫胺素生物合成的系统的遗传分析已经确定了一组五个条件硫胺素轴养菌是有缺陷的铁-硫簇代谢。总的来说，这些位点似乎是必要的铁贩运，氧化损伤的Fe-S簇的修复。概述了一系列的实验，以解决这些蛋白质（ApbE，ApbC和RseC）的特定生化功能。本文描述的项目分为两个相似和重叠的目标，最终将定义这些蛋白质和其他参与Fe-S代谢的蛋白质之间的关系。这些目标的完成将需要在体内和体外实验，严格应用生物化学，生物物理，遗传和生理技术。本提案中提出的研究的长期目标是促进对代谢整合的理解，特别是Fe稳态。为了达到这一目标，我们必须增加我们对新陈代谢的生化成分以及它们之间存在的联系的知识。这些工作不仅有助于基因组的严格注释，而且为铁和自由基代谢的继续研究提供了基础。细胞代谢是在任何给定时间在活细胞中发生的所有化学反应的总和。就像互联网或经济一样，新陈代谢是一个网络或系统，因此微小的变化，例如营养素的去除，可能会产生深远的影响。这项工作的目的是了解这些化学反应之间的联系，以便预测如果系统以某种方式受到干扰（癌症，饥饿，疾病等），将会遇到的影响。