Metabolic Control in a Dynamic Environment

描述（由申请人提供）：细胞在恒定的环境中生长，如实验室培养，可以自由地将其所有资源用于生长和分裂，并经常达到其最大生长速率。然而，在自然界中，细胞很少经历静态状态。无论是作为单个细胞存在，还是作为大型多细胞生物的一部分存在，自然活细胞都必须应对周围环境的频繁变化。为了在动态环境中生存，细胞配备了基因网络，使其能够在变化的条件下继续生长。这种灵活性是有代价的，经历环境变化的细胞通常不能达到最快的生长速度。为了充分了解细胞生长和动态代谢之间的界面，我们必须研究细胞在变化的环境中生长的情况。在拟议的项目中，我们将使用酵母半乳糖网络作为环境敏感基因调控的范例，以了解细胞如何平衡对生长介质变化的响应需求和维持生长的压力。在整个研究中，我们将依靠创新的微工具在精确控制的动态环境中生长和观察单细胞。我们收集的动态数据将为一组数学模型提供信息，该模型将用于识别半乳糖网络中的调节关键点，然后将使用先前建立的分子生物学技术对其进行严格测试。这种多学科的方法将增强我们识别基因调控新机制的能力，这些机制特别影响细胞感知生长环境的方式，这在标准实验室培养中很难观察到。我们的下一个目标将是研究半乳糖网络固有的调节环对细胞对可用碳源的敏感性的影响，并确定它们如何影响半乳糖生长的代谢成本。在以前的工作中，我们观察到几个半乳糖网络基因的转录本受到空间调控。在第二个目标中，我们将关注这些转录本的定位，以验证基因表达的空间调控可以导致细胞对环境信号反应的新时间控制的假设。我们的初步数据表明，半乳糖蛋白的合成受到特定细胞周期调节因子mRNA的负反应。在第三个目标中，我们将使用排队理论来解释特定转录本之间的翻译竞争如何导致细胞分裂和半乳糖代谢的耦合，并导致当葡萄糖不可用时生长速度较慢。最后，在第四个目标中，我们将通过确定在不同程度的竞争性蛋白质合成背景下网络的鲁棒性来研究半乳糖途径的调节回路的功能。这个项目的成功完成将导致我们对细胞如何解决在不可预测的环境中生存的普遍生物学问题的理解的进步。这项工作将与理解根据环境因素平衡生长速率的机制特别相关，因为这在癌症生物学、组织模式和胚胎发育中很重要。1

DESCRIPTION (provided by applicant): Cells growing in a constant environment, such as a laboratory culture, are free to dedicate all of their resources to growth and division and often reach their maximal growth rate. However, in the natural world, cells rarely if ever experience static conditions. Whether they exist as a single cell or as part of a large multicellular organism, natural-living cells must cope with frequent changes to their surroundings. To survive in a dynamic environment, cells are equipped with gene networks that allow growth to continue in spite of changing conditions. This exibility comes at a price, and cells experiencing environmental uctuations usually do not attain their fastest growth rate. To fully understand the interface between cell growth and dynamic metabolism, we must study cells as they grow in a changing environment. In the proposed project, we will use the yeast galactose network as a paradigm of environment-sensitive gene regulation to ask how cells balance the need to respond to changes in the growth medium against the pressure to maintain growth. Throughout this study, we will rely on innovative microuidic tools to grow and observe single cells in precisely controlled dynamic environments. The dynamic data we collect will inform a set of mathematical models that will be used to identify key points of regulation in the galactose network, which will then be rigorously, tested using previously established molecular biology techniques. This multi-disciplinary approach will bolster our ability to identify new mechanisms of gene regulation that specially inuence the way cells perceive the growth environment, which are diffcult to observe in standard laboratory cultures. Our rst aim will be to study the eects of regulatory loops inherent to the galactose network on the sensitivity of cells to available carbon sources, and to determine how they contribute to the metabolic cost of growth on galactose. In previous work, we observed that the transcripts of several galactose network genes are spatially regulated. In the second aim, we will focus on the localization of these transcripts to test the hypothesis that the spatial regulation of gene expression can lead to ne temporal control in the cellular response to environmental signals. Our preliminary data show that the synthesis of galactose proteins is negatively eected by the mRNA of a specic cell cycle regulator. In the third aim, we will use queuing theory to explain how a competition for translation between specic transcripts can lead to a coupling of cell division and galactose metabolism and result in slower growth rates when glucose is unavailable. Finally, in the fourth aim, we will study the function of the regulatory loops of the galactose pathway by determining the robustness of the network in the context of varying degrees of competitive protein synthesis. The successful completion of this project will lead to advances in our understanding of how cells solve the universal biological problem of survival in an unpredictable environment. This work will be particularly relevant to understanding the mechanisms involved in balancing growth rate according to environmental cues, as is important in cancer biology, tissue patterning, and embryonic development. 1