New Cell Type-Specific Data Sets and Computational Approaches for Plant Stress Biology

干旱是作物减产的主要原因之一。因此，了解植物如何应对水分限制是很重要的。在理解保卫细胞方面已经取得了很大进展，保卫细胞是定义气孔的细胞类型。这些是叶表面的毛孔，根据各种信号而打开和关闭，包括植物的水分状况。在干旱情况下，气孔必须起到平衡植物“饥饿”(大气中的二氧化碳仍然需要通过气孔进入叶片才能进行光合作用)和“渴”(在干旱情况下接近保存水分的气孔)的作用。2009年，Sean Cutler，Erwin Grill及其同事发现了ABA共同受体PYR1和PYR1样家族，以及Julian Schroeder和Sally Assmann等团队的广泛基因工作，有助于阐明保卫细胞中的信号网络。 从特定细胞类型中分离遗传物质的新方法，如Henikoff实验室和Bailey-Serres实验室分别在植物中建立的完整(分离特定细胞类型的细胞核)和靶向TRAP(翻译核糖体亲和纯化)方法，使人们能够前所未有地了解特定细胞类型的生物反应。普罗瓦特实验室提出的研究计划旨在利用这些工具在保卫细胞、转录和表观基因组水平上了解植物对干旱的反应。此外，我们将研究干旱激素脱落酸可能介导的蛋白质-蛋白质相互作用，最后，我们将研究保卫细胞表达的信号蛋白活性部位附近的多态对这些蛋白质功能的影响。无论如何，我们将继续创造创新的“网络基础设施”社区资源/“应用程序”，供我自己的实验室和世界各地的植物研究人员使用。虽然我们已经开发了一个初步的框架，用于探索从千米到纳米尺度的数据集，但我们将在这些尺度之间建立联系，并使数据搜索变得容易，这样就可以解决像这样的问题，如“这个特定的小分子能否与任何已解决或预测的蛋白质三级结构对接，以及多态是否会影响其结合？”可能会被问到。 意义：这三个项目的植物内/体外部分将产生几个新的候选耐逆基因，这些基因可以很容易地在农业上部署。我的实验室开发的网络基础设施将使基于大型数据集的新见解成为可能，将利用这些由公共资金资助的数据集的价值，并将使人们能够更好地了解植物生物学。在气候变化的情况下，这对于到2050年养活90亿人至关重要。

Drought is one of the primary causes of reduced crop yields. Understanding how plants respond to water limitation is therefore important. Much progress has been made on understanding guard cells, the cell types that define the stomata. These are pores on the leaf surface that open and close in response to a variety of signals, including the water status of the plant. Under drought, stomata must act to balance a plant's “hunger” (CO2 from the atmosphere still needs to enter the leaf through the stomata for photosynthesis to occur) with its “thirst” (stomata close to conserve water under drought). The discovery of the ABA co-receptors PYR1 and PYR1-like family in 2009 by Sean Cutler, Erwin Grill, and colleagues, along with extensive genetic work by, among others, Julian Schroeder's and Sally Assmann's groups, has helped towards elucidation of the signaling networks in guard cells. New methods for the isolation of genetic material from specific cell types, such as INTACT (isolation of nuclei tagged in specific cell types) and targeted TRAP (translating ribosome affinity purification), as established in plants by the Henikoff and Bailey-Serres Laboratories, respectively, are allowing unprecedented understanding of biological responses at the resolution of specific cell types. The Provart Lab's proposed research program aims to use such tools to understand how plants react to drought at the level of guard cell transcriptional and epigenomic responses. Further, we will investigate predicted protein-protein interactions that could be mediated by the drought hormone abscisic acid, and, finally, we will investigate polymorphisms in the vicinity of active sites of guard cell-expressed signaling proteins for their effect on the function of these proteins. In all cases, we will continue to create innovative “cyberinfrastructural” community resources / “apps” for use by my own lab and by plant researchers worldwide. While we have developed an initial framework for exploring data sets from the kilometer to nanometer scales, we will create linkages between these scales and enable easy searching of the data so that questions such as “could this particular small molecule dock with any solved or predicted protein tertiary structure, and might a polymorphism affect its binding?” may be asked. Significance: The in planta/in vitro part of these three projects will result in several novel candidate stress-tolerance genes that can be readily deployed agriculturally. The cyberinfrastructure developed by my laboratory will enable new insights based on large data sets, will leverage the value of these publicly-funded data sets, and will permit a better understanding of plant biology. This is critical to feeding 9 billion people by 2050 under a changing climate.