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.
