Functional Genomics of Stress Defense in Yeast

酵母应激防御的功能基因组学

• 批准号: 8644804
• 负责人: AUDREY P GASCH
• 金额: $ 31.66万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-05-01 至 2017-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8644804
• 关键词: Aging; Algorithms; Biology; Cell Cycle Progression; Cell Death; Cells; Cellular Stress; Collaborations; Complex; Computational Biology; DNA-Protein Interaction; Data; Data Analyses; Data Set; Defect; Detection; Disease; Ensure; Eukaryota; Eukaryotic Cell; Failure; Fostering; Foundations; Gene Expression; Gene Expression Profile; Generations; Genetic; Genomics; Goals; Growth; Health; Homeostasis; Human; Left; Linear Programming; Link; Malignant Neoplasms; Maps; Mass Spectrum Analysis; Mediating; Metabolism; Methodology; Modeling; Molecular; Molecular Biology; Monitor; Mutation; Network-based; Neurologic; Organism; Orthologous Gene; Osmotic Shocks; Output; Phosphorylation; Phosphotransferases; Physiological; Physiological Processes; Physiology; Process; Proteins; Proteome; Proteomics; RNA Binding; Reaction; Resistance; Saccharomyces cerevisiae; Signal Pathway; Signal Transduction; Signaling Molecule; Signaling Protein; Sodium Chloride; Specificity; Stress; Substrate Interaction; System; Testing; Time; Toxin; Transcript; Validation; Work; Yeasts; base; biological adaptation to stress; cell type; functional genomics; human disease; improved; innovation; insight; mutant; public health relevance; response; stress tolerance; stressor

DESCRIPTION (provided by applicant): Cellular stress results when external conditions or internal defects perturb cellular homeostasis. If left unattended, this stress can dramatically alter normal physiology, causing either cell death or rampant growth without normal control mechanisms. Cells therefore have intricate signaling networks that integrate and transmit the proper signals to mediate a multi-faceted response. These responses often involve coordinated changes in cell-cycle progression, gene expression, protein localization and function, and metabolism. How cells orchestrate multiple downstream processes is poorly understood. Furthermore, many of the players in this important regulatory network, and the interactions between them, remain unknown. This proposal aims to elucidate the complex global signaling network that orchestrates stress responses in the model eukaryote Saccharomyces cerevisiae. The work will apply mutant transcriptome profiling, phosphoproteomic analysis, computational biology, and genetics and molecular biology. A key innovation is generation of functional genomic and proteomic data collected under stress conditions, to aid in the computational network inference from available large-scale yeast datasets. Aim 1 will refine and apply an integer linear programming approach that takes transcriptome profiles and functional data to infer the global regulatory network that coordinates genomic expression after osmotic or DTT reductive stress. Combined with molecular validation of the network, the end result will be a detailed, directional global network of signaling molecule that coordinate genomic expression in response to different stresses. Comparing and contrasting the responses to two distinct stressors will reveal condition-specific regulators and common players in the network. Aim 2 will take a complementary approach to interrogate phospho-proteomic networks. Quantitative changes in the phospho-proteome will be identified by mass spectrometry, in wild-type and mutant cells lacking implicated kinases as cells respond to osmotic or DTT stress. The resulting phospho-networks will overlap with the signaling networks from Aim 1 but will include unique regulators of diverse physiological processes. Integrating the results from both aims will present a unified view of the signaling network that coordinates gene expression, protein phosphorylation, and physiological responses to several conditions. Together, this work will provide many new insights into stress biology and signaling, by identify new regulators of eukaryotic stress responses, uncovering the connections between them, and illuminating the mechanisms of network rewriting and information flow that coordinate stress responses. Because many yeast signaling proteins have human orthologs linked to disease, these results will provide an important backdrop for directed study in human cells.

描述（由申请人提供）： 当外部条件或内部缺陷扰动细胞稳态时，会导致细胞应力。如果无人看管，这种压力会大大改变正常的生理，从 或没有正常控制机制的猖ramp的生长。因此，细胞具有复杂的信号网络，可以整合和传输适当的信号以介导多面响应。这些反应通常涉及细胞周期进展，基因表达，蛋白质定位和功能以及代谢的协调变化。细胞如何编排多个下游过程的理解很少。此外，这个重要的监管网络中的许多参与者以及它们之间的相互作用仍然未知。该提案旨在阐明复杂的全球信号网络，该网络在酿酒酵母的真核生糖果疗法中策划了应力反应。这项工作将采用突变的转录组分析，磷酸蛋白质组学分析，计算生物学以及遗传学和分子生物学。一个关键的创新是在应力条件下收集的功能基因组和蛋白质组学数据的产生，以帮助从可用的大型酵母数据集中进行计算网络推断。 AIM 1将完善并采用整数线性编程方法，该方法采用转录组轮廓和功能数据来推断全球调节网络，该网络在渗透或DTT还原应力后协调基因组表达。结合网络的分子验证，最终结果将是一个详细的，定向的信号分子网络，该网络响应不同的应力，协调基因组表达。比较和对比对两个不同的压力源的响应将揭示特定于条件的调节剂和网络中的普通参与者。 AIM 2将采用一种互补方法来询问磷酸化 - 蛋白质网络。磷酸化 - 蛋白蛋白质组的定量变化将通过质谱，在野生型和突变细胞中鉴定，因为细胞对渗透或DTT胁迫反应，缺乏激酶。由此产生的磷酸化网络将与AIM 1的信号网络重叠，但将包括各种生理过程的独特调节剂。整合两个目标的结果将呈现对信号网络的统一观点，该视图辅助基因表达，蛋白质磷酸化以及对几种条件的生理反应。这项工作将通过确定真核压力反应的新调节因子，揭示它们之间的联系，并阐明网络重写和信息流的机制以协调压力响应的机制，从而为压力生物学和信号传导提供许多新的见解。由于许多酵母信号蛋白具有与疾病相关的人类直系同源物，因此这些结果将为人类细胞中的指导研究提供重要的背景。