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

植物逆境生物学的新细胞类型特异性数据集和计算方法

• 批准号: RGPIN-2016-06483
• 负责人: Provart, Nicholas
• 金额: $ 5.25万
• 依托单位: University of Toronto
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2016
• 资助国家: 加拿大
• 起止时间: 2016-01-01 至 2017-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=616340
• 关键词: New; Cell; Type; Specific; Data

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.

干旱是作物减产的主要原因之一。因此，了解植物对水分限制的反应非常重要。对保卫细胞（定义气孔的细胞类型）的理解已经取得了很大进展。这些是叶片表面的气孔，它们会根据各种信号（包括植物的水分状况）打开和关闭。在干旱的情况下，气孔必须采取行动来平衡植物的“饥饿”（大气中的CO2仍然需要通过气孔进入叶片进行光合作用）和“干渴”（气孔关闭以保存干旱下的水分）。2009年，Sean Cutler，Erwin Grill和同事发现了阿坝辅助受体PYR 1和PYR 1样家族，沿着Julian Schroeder和Sally Assmann等人的广泛遗传工作，有助于阐明保卫细胞中的信号网络。 用于从特定细胞类型分离遗传物质的新方法，例如由Henikoff和Bailey-Serres实验室分别在植物中建立的INTACT（在特定细胞类型中标记的细胞核的分离）和靶向TRAP（翻译核糖体亲和纯化），正在允许前所未有地理解在特定细胞类型的分辨率下的生物反应。Provart实验室提出的研究计划旨在使用这些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，我们将研究预测的蛋白质-蛋白质相互作用，可以介导的干旱激素脱落酸，最后，我们将研究多态性的保卫细胞表达的信号蛋白的活性位点附近的这些蛋白质的功能的影响。在所有情况下，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，并使数据的搜索变得容易，以便提出诸如“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，多态性是否会影响其结合？”可以问。 重要性：这三个项目的植物/体外部分将产生几个新的候选耐胁迫基因，可以很容易地部署在农业上。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，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年在不断变化的气候下养活90亿人至关重要。