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

多细胞生物有不同的器官，需要作为一个完整的系统进行交流，才能使有机体茁壮成长。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，根在土壤中寻找养分需要树枝提供能量，在那里发生光合作用。这种器官间的交流使植物的根能够作为一个综合系统在不断变化的环境中快速响应和觅食营养。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、系统观点。在拟南芥模型中使用一种特殊的分根实验设计，这项工作将推导出控制植物对氮素吸收和同化的系统反应的分子和信号的假设。这些研究将确定参与根茎通讯的新的器官间信号，包括mRNAs、小RNAs和激素。从该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中的养分捕获，从而降低农业中使用的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，可用于剖析跨植物生物学的系统范围的器官间信号。系统生物学的一个主要目标是将生物体作为一个综合系统来预测如何对扰动作出反应。对于多细胞、多器官系统，需要器官内和器官间信号的协调才能对环境扰动做出综合反应。这笔赠款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能够在复杂的环境中积极寻找限制生长的营养氮(N)。这种方法的新奇之处在于“分根”系统，它可以报告全身(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，每个根的一半暴露在不同的N环境中。这种设置先前已被用来发现两种不同类型的系统N信号：i)来自暴露在N耗尽环境中的根-半部的“N-需求”信号，其特定地刺激暴露在N-全环境中的远端根中的侧根(LR)生长；ii)来自N-全环境中的根-半部的N-供应信号，其特定地抑制暴露在N-完全环境中的远端根中的LR生长。从这种设置中进行的微阵列研究发现了根-冠-根传递系统在整个系统范围内传递氮供应和氮需求的证据。这项建议的目标是在四个相关的目标中确定这些系统的N供应和N需求信号以及参与这一继发的分子成分。首先，为了产生器官间信号的因果模型，RNA-seq将被用于监测暴露在异质N环境中后作为空间(器官)和时间函数的mRNA和小RNA(目标1)。下一步，器官间旅行的RNA将在韧皮部-植物的“信息高速公路”(目标2)中被捕获。在目标3中，这些数据集将被整合和建模，以确定在系统器官间N信号中涉及特定信号(激素、sRNA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，在那里将研究它们在根N觅食和N吸收中的作用。联合的AIMS将检验三个非排他性假说：1.地上部反应：受系统N信号影响的特定地上部基因/过程需要调节根对异质N环境的反应。2.运输信号(S)：特定的长距离信号(激素、mRNAs或sRNAs)参与系统的、器官间的N信号。3.根反应：根中的长距离信号和局部N反应基因的特定组合触发了根在异质N环境中的N觅食。对于科学界，该项目将为系统范围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理解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中的养分捕获。最终目标是设计出提高氮肥利用效率的植物，从而降低农业中使用的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.