Integrated Metabolism in Methylobacterium extroquens AM1

外来甲基杆菌 AM1 的综合代谢

• 批准号: 7764769
• 负责人: Mary E Lidstrom
• 金额: $ 44.27万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-02-01 至 2011-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7764769
• 关键词: Address; Bacteria; Biochemical Pathway; Biological Models; Biomass; Budgets; Carbon; Cells; Comparative Study; Complement component C1s; Complex; Coupled; Data; Data Set; Energy Metabolism; Enzymes; Equilibrium; Formaldehyde; Formate dehydrogenase; Funding; Genetic; Genetic Transcription; Genome; Glutathione; Glyoxylates; Goals; Grant; Growth; Iron; Kinetics; Ligase; Measurement; Measures; Metabolic; Metabolism; Methanol; Methylobacterium; Methylobacterium extorquens; Modeling; Modification; National Institute of General Medical Sciences; Output; Pathway interactions; Physiological; Property; Proteins; Regulation; Role; Staging; Stress; Succinates; System; Testing; Transcript; Work; base; biological adaptation to stress; carbon compound; cost; enzyme activity; fatty acid metabolism; glyoxylate; insight; metabolic abnormality assessment; response; tool

DESCRIPTION (provided by applicant): Metabolism in bacteria occurs via a set of complex, dynamic, and interconnected metabolic steps (metabolic modules). The outputs of such metabolic systems depend on the interplay between the genetic circuits in the cell, which generate proteins, and the metabolic circuits, which generate flux and metabolite pools. Understanding how this complex system functions in the cell is the goal of integrated metabolism studies. Global "omics"-based approaches coupled to metabolic models and physiological insight are setting the stage for understanding how the metabolic network functions as an integrated system. Methylobacterium extorquens is a facultative methylotrophic bacterium, which has the property of two dramatically different modes of growth: growth on one-carbon (C1) compounds is reducing-power limited, while growth on multi-carbon compounds is energy-limited. In addition, through past NIH-funded work on this bacterium, a suite of computational and genetic tools and multivariate "omics" datasets are available. Therefore, this bacterium is becoming an attractive model system in which to ask fundamental questions regarding metabolic integration, using comparative studies of different metabolic conditions. We propose to analyze how methylotrophic metabolism functions as an integrated system in M. extorquens. Our data to date show that at steady-state, the cells are in balance, while during perturbations, the metabolic network is shifted out of balance and the cells respond dramatically at the transcriptional, flux and metabolite levels. The response "resets" the metabolic state at a different level, and the cells return to a balanced state. In this next project period, we will address how this response occurs at the metabolic module level, and carry out a set of manipulations to probe specific metabolic states and response scenarios. The specific aims of this project are as follows: 1. Determine metabolic states of the cell. Linkages between central methylotrophic metabolism and other core metabolic functions that have been identified will be detailed, including growth rate, stress response, iron acquisition, and fatty acid metabolism. Metabolic states for all known modules will be determined by measuring transcripts, proteins, enzyme activities, fluxes, and metabolite pools. A set of criteria will be identified that define each metabolic state. 2. Analyze how the metabolic state changes in response to perturbations. Using the same set of measurements as in specific aim 1, we will determine how metabolic modules respond to changes in growth rate and flux of substrates and how they change when genetic modifications cause altered metabolic states, such as altered reducing power balance and altered flux through specific metabolic modules. The data generated in specific aim 1 and 2 will be analyzed to determine how the metabolic and genetic circuits are integrated. This study is expected to result in new principles in metabolic integration, as well new insights into C1 metabolism.

描述（由申请人提供）：细菌中的代谢通过一组复杂、动态和相互关联的代谢步骤（代谢模块）发生。这种代谢系统的输出取决于细胞中产生蛋白质的遗传回路与产生通量和代谢物库的代谢回路之间的相互作用。了解这个复杂的系统如何在细胞中发挥作用是综合代谢研究的目标。全球“组学”为基础的方法，结合代谢模型和生理学的洞察力，为理解代谢网络如何作为一个综合系统发挥作用奠定了基础。扭脱甲基杆菌是一种兼性甲基营养细菌，其具有两种显著不同的生长模式的性质：在一碳（C1）化合物上的生长是还原力有限的，而在多碳化合物上的生长是能量有限的。此外，通过过去NIH资助的对这种细菌的研究，可以获得一套计算和遗传工具以及多变量“组学”数据集。因此，这种细菌正在成为一个有吸引力的模型系统，在其中询问有关代谢整合的基本问题，使用不同代谢条件的比较研究。我们建议分析如何甲基营养代谢功能作为一个完整的系统在M。扭体我们迄今为止的数据表明，在稳态下，细胞处于平衡状态，而在扰动期间，代谢网络失去平衡，细胞在转录，通量和代谢物水平上做出显着反应。这种反应将代谢状态“重置”到不同的水平，细胞恢复到平衡状态。在下一个项目期间，我们将解决这种反应如何在代谢模块水平上发生，并进行一系列操作来探测特定的代谢状态和反应场景。本项目的具体目标如下：1.确定细胞的代谢状态。中央甲基营养代谢和其他核心代谢功能之间的联系，已被确定将详细，包括生长速度，应激反应，铁的收购，和脂肪酸代谢。所有已知模块的代谢状态将通过测量转录物、蛋白质、酶活性、通量和代谢物池来确定。将确定一组定义每种代谢状态的标准。2.分析代谢状态如何响应扰动而变化。使用与具体目标1中相同的一组测量，我们将确定代谢模块如何响应生长速率和底物通量的变化，以及当遗传修饰导致代谢状态改变时它们如何改变，例如改变还原能力平衡和改变通过特定代谢模块的通量。具体目标1和2中生成的数据将被分析，以确定代谢和遗传回路是如何整合的。这项研究预计将导致代谢整合的新原则，以及对C1代谢的新见解。