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

干旱是农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非常重要。在理解保卫细胞（定义气孔的细胞类型）方面已经取得了很大进展。这些是叶子表面上的孔隙，根据各种信号（包括植物的水分状况）而打开和关闭。在干旱情况下，气孔必须平衡植物的“饥饿”（大气中的二氧化碳仍然需要通过气孔进入叶子才能进行光合作用）和“渴”（在干旱情况下气孔接近保存水分）。 Sean Cutler、Erwin Grill 及其同事于 2009 年发现了 ABA 共受体 PYR1 和 PYR1 样家族，再加上 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。 Henikoff 和 Bailey-Serres 实验室分别在植物中建立了从特定细胞类型中分离遗传物质的新方法，例如 INTACT（分离特定细胞类型中标记的细胞核）和靶向 TRAP（翻译核糖体亲和纯化），这使得我们能够以前所未有的方式了解特定细胞类型分辨率下的生物反应。普罗瓦尔特实验室提出的研究计划旨在利用此类工具来了解植物如何在保卫细胞转录和表观基因组反应水平上对干旱做出反应。此外，我们将研究预测的可由干旱激素脱落酸介导的蛋白质-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位点附近的多态性及其对这些蛋白质功能的影响。在所有情况下，我们将继续创建创新的“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用于探索从千米到纳米尺度的数据集的初始框架，但我们将在这些尺度之间建立联系，并能够轻松搜索数据，以便解决诸如“这种特定的小分子是否可以与任何已解决或预测的蛋白质三级结构对接，以及多态性是否会影响其结合？”等问题。可能会被问到。 意义：这三个项目的植物体内/体外部分将产生几种新的候选抗逆基因，这些基因可以很容易地在农业上应用。我的实验室开发的网络基础设施将基于大数据集提供新的见解，将利用这些公共资助的数据集的价值，并将允许更好地了解植物生物学。这对于到 2050 年在气候变化的情况下养活 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.