Prospecting for Resources: A Systems Integration of Local and Systemic Nutrient Signaling

多细胞生物有不同的器官，它们需要作为一个完整的系统进行交流，以使有机体茁壮成长。例如，在动物身上，肾脏中产生的化合物可以调节心脏功能。在植物中，根部在土壤中觅食养分需要由芽提供能量，而芽是光合作用发生的地方。这种器官间的交流使植物根系作为一个完整的系统能够在不断变化的环境中快速响应和觅食营养物质。这个项目代表了植物适应不断变化的环境的第一个器官间，系统的观点。在拟南芥模型中使用一种特殊的裂根实验设计，这项工作将得出控制植物对氮吸收和同化的系统反应的分子和信号的假设。这些研究将确定新的器官间信号，包括mrna、小rna和激素。从这个项目中获得的新的生物学认识有可能为作物的基因改造提供信息，以改善现实世界环境中土壤的养分捕获，从而降低农业中使用氮肥的环境和能源成本。该项目还将开发新的数学模型和集成的理论框架，可用于解剖植物生物学系统范围内的器官间信号传导。系统生物学的一个主要目标是预测一个有机体如何作为一个综合系统对扰动作出反应。对于多细胞、多器官系统，需要协调器官内和器官间的信号传导来对环境扰动进行综合响应。这项资助将测试器官间系统信号和局部信号的相互作用如何使植物在复杂环境中主动觅食生长限制营养氮(N)。该方法的新颖之处在于“分裂-根”系统，它可以报告系统（器官间）和局部（器官内）信号，这在标准设置中是不可能的。在分根系统中，单个植物的根被分开，每半根暴露在不同的氮环境中。这种设置以前被用于发现两种不同类型的系统n信号：i)来自暴露于“缺氮环境”的根半的“n需求”信号，该信号特异性地刺激暴露于缺氮环境的远端根的侧根（LR）生长，ii)来自富氮环境的根半的“n供应”信号，该信号特异性地抑制暴露于缺氮环境的远端根的LR生长。该装置的微阵列研究发现了根-枝-根中继系统在全系统范围内通信n供应和n需求的证据。本提案的目标是在四个相关目标中确定这些系统的n供应和n需求信号和参与该中继的分子成分。首先，为了建立器官间信号传导的因果模型，RNA-seq将用于监测mRNA和小rna在暴露于异质n环境后作为空间（器官）和时间的功能（Aim 1）。接下来，在韧皮部（植物的“信息高速公路”）中捕获器官间旅行的rna（目标2）。在Aim 3中，这些数据集将被整合和建模，以确定在系统器官间n信号传导中涉及特定信号（激素、sRNAs和mRNA/蛋白质）的因果靶基因对。候选信号和基因将在Aim 4中进行实验验证，届时将研究它们在根系n -觅食和n -吸收中的作用。综合目标将检验三个非排他的假设：茎部响应：需要受系统n信号影响的特定茎部基因/过程来介导根对异质n环境的响应。2. 运输信号：特定的远距离信号（激素、mrna或srna）参与了系统的、器官间的n信号传导。3. 根系响应：根系长距离信号与局部n响应基因的特定组合触发了异质性n环境下根系的n觅食。对于科学界来说，该项目将为全系统的器官间信号传递开发新的数学模型和综合理论框架。此外，从这个项目中获得的新的生物学认识有望为作物的基因改造提供信息，以改善现实世界环境中土壤的营养捕获。最终目标是设计提高氮利用效率的植物，从而降低农业中使用氮肥的环境和能源成本。

Multicellular organisms have distinct organs that need to communicate as an integrated system in order for the organism to thrive. In animals, for example, compounds produced in the kidney regulate heart function. In plants, root foraging for nutrients in the soil requires energy provided by shoots, where photosynthesis occurs. This inter-organ communication enables plant roots to rapidly respond to and forage for nutrients in a changing environment as an integrated system. This project represents the first inter-organ, systems-view of plant adaptation to a changing environment. Using a special split-root experimental design in the model Arabidopsis, this work will derive hypotheses for the molecules and signals controlling a plant's systemic response to nitrogen uptake and assimilation. The studies will identify novel inter-organ signals involved in root-shoot communication including mRNAs, small RNAs and hormones. The new biological understanding gained from this project has the potential to inform genetic modification of crops for improved nutrient-capture in soil in a real world environment, thereby reducing the environmental and energy cost of nitrogen fertilizer used in agriculture. This project will also develop novel mathematical models and an integrated theoretical framework that can be used to dissect systems-wide inter-organ signaling across plant biology. A major goal of systems biology is to predictively model how an organism will respond to perturbations as an integrated system. For multicellular, multi-organ systems, coordination of intra- and inter-organ signaling is required to mount an integrated response to environmental perturbations. This grant will test how the interplay of inter-organ systemic signaling and local signaling enable a plant to actively forage for the growth-limiting nutrient nitrogen (N) in a complex environment. The novelty of the approach is the "split-root" system, which can report on both systemic (inter-organ) and local (intra-organ) signaling which is not possible in standard set-ups. In the split-root system, roots of a single plant are split and each root-half is exposed to a different N-environment. This set-up has previously been used to discover two distinct types of systemic N-signals: i) a "N-demand" signal from the root-half exposed to an "N-deplete environment that specifically stimulates lateral root (LR) growth in the distal root exposed to an N-replete environment, ii) an N-supply" signal from the root-half in the N-replete environment that specifically represses LR growth in the distal root exposed to an N-deplete environment. Microarray studies from this set-up uncovered evidence for a root-shoot-root relay system communicating N-supply and N-demand systems-wide. The goal of this proposal is to identify these systemic N-supply and N-demand signals and molecular components involved in this relay in four related aims. First, to generate causal models for inter-organ signaling, RNA-seq will be used to monitor mRNA and small RNAs as a function of space (organ) and time after exposure to a heterogeneous N-environment (Aim 1). Next, inter-organ traveling RNAs will be captured in phloem - the plant "information highway" (Aim 2). In Aim 3, these datasets will be integrated and modeled to identify causal target gene pairs that implicate specific signals (hormones, sRNAs and mRNA/proteins) in systemic inter-organ N-signaling. Candidate signals and genes will be experimentally validated in Aim 4, where their role in root N-foraging and N-uptake will be examined. The combined aims will test three non-exclusive hypotheses: 1. Shoot Response: specific shoot genes/processes affected by systemic N-signaling are required to mediate root responses to a heterogeneous N-environment. 2. Trafficking Signal(s): specific long-distance signals (hormones, mRNAs, or sRNAs) are involved in systemic, inter-organ N-signaling. 3. Root Response: a specific combination of long-distance signals and local N-response genes in roots triggers root N-foraging in a heterogeneous N-environment. For the scientific community, this project will develop novel mathematical models and an integrated theoretical framework for systems-wide inter-organ signaling. Moreover, the new biology understanding gained from this project promises to inform genetic modification of crops for improved nutrient-capture in soils in a real world environment. The ultimate goal is to engineer plants with improved nitrogen use efficiency, hence reducing the environmental and energy cost of nitrogen fertilizer used in agriculture.