The primary goal of the proposed research is to use a systems biology approach to collectively analyze and integrate time-dependent data from the transcriptome, metabolome, and fluxome components of the N- regulatory network controlling N-assimilation in Arabidopsis. This integrative approach will allow us to dynamically model the flow of N-signal propagation through the N-regulatory network on a systems-wide level and identify the transcriptional cascade involved in this regulation. This goal will be achieved through four aims: 1. Creation of high-resolution dynamic transcriptome datasets to generate a time-dependent nitrogen regulatory network, by performing microarray analysis on Arabidopsis roots and shoots treated with nitrate over a time course. 2. Quantification of metabolite levels and metabolic flux in the N-assimilatory network in response to N-signal, using stable isotope labeled N15 over a time course. 3. Integration of transcriptome, metabolome, and fluxome data to create a time-dependent dynamic network model for the control of N- uptake/assimilation, using a series of analytical techniques including lag correlation, linear regression, and machine learning (state space analysis). 4. Functional validation of regulatory network predictions by testing model generated hypotheses with T-DNA mutants and inducible expression systems. The overriding hypothesis being tested is that inorganic-N signals (nitrate) activate motifs involved in regulating nitrate uptake, reduction and assimilation into organic-N (Glu/Gln), used for biosynthetic reactions. The organic-N products (Glu/Gln) in turn activate motifs controlling Asn synthesized for N-storage, and repress ones controlling N- uptake/assimilation. The proposed research will allow me to identify the regulatory genes responding to these inorganic and organic N-signals that regulate genes in the N-uptake and assimilation pathways by integrating genome wide transcriptomic data with metabolomic data. The synthesis of these aims should allow for modeling, predicting and testing how perturbations of the """"""""system"""""""" may be used to enhance N-use efficiency, which impacts energy-use (fertilizers/biofuels), nitrate contamination of the environment and human nutrition.

Public Health Relevance

The long-term goal of the systems approach described in this proposal is to model and predictively manipulate gene regulatory networks affecting uptake/assimilation of inorganic nitrogen into amino acids to improve nitrogen-use-efficiency. This would decrease energy consumption, reduce ground water contamination by nitrates (Health and Environment) and improve seed yield, with implications for human health (Nutrition) and biofuels (Energy). Moreover, the systems biology approach and the tools that will be developed in this project can be applied to any species for which genome data is available, which will enable researchers to model and manipulate a broad spectrum of regulatory circuits in biology with potential medical and pharmaceutical applications.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Postdoctoral Individual National Research Service Award (F32)
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Special Emphasis Panel (ZRG1-F08-E (20))
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Hagan, Ann A
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New York University
Schools of Arts and Sciences
New York
United States
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Varala, Kranthi; Marshall-Colón, Amy; Cirrone, Jacopo et al. (2018) Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. Proc Natl Acad Sci U S A 115:6494-6499
Medici, Anna; Marshall-Colon, Amy; Ronzier, Elsa et al. (2015) AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nat Commun 6:6274
Varala, Kranthi; Li, Ying; Marshall-Colón, Amy et al. (2015) ""Hit-and-Run"" leaves its mark: catalyst transcription factors and chromatin modification. Bioessays 37:851-6
Para, Alessia; Li, Ying; Marshall-Colón, Amy et al. (2014) Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Proc Natl Acad Sci U S A 111:10371-6
Marshall-Colon, Amy; Sengupta, Neelanjan; Rhodes, David et al. (2014) Simulating labeling to estimate kinetic parameters for flux control analysis. Methods Mol Biol 1090:211-22
Krouk, Gabriel; Lingeman, Jesse; Colon, Amy Marshall et al. (2013) Gene regulatory networks in plants: learning causality from time and perturbation. Genome Biol 14:123