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Review
. 2016 Oct 10;5(4):39.
doi: 10.3390/plants5040039.

Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches

Perrin H Beatty  1 , Matthias S Klein  2 , Jeffrey J Fischer  3 , Ian A Lewis  4 , Douglas G Muench  5 , Allen G Good  6
Affiliations
Review

Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches

Perrin H Beatty et al. Plants (Basel). .

Abstract

A comprehensive understanding of plant metabolism could provide a direct mechanism for improving nitrogen use efficiency (NUE) in crops. One of the major barriers to achieving this outcome is our poor understanding of the complex metabolic networks, physiological factors, and signaling mechanisms that affect NUE in agricultural settings. However, an exciting collection of computational and experimental approaches has begun to elucidate whole-plant nitrogen usage and provides an avenue for connecting nitrogen-related phenotypes to genes. Herein, we describe how metabolomics, computational models of metabolism, and flux balance analysis have been harnessed to advance our understanding of plant nitrogen metabolism. We introduce a model describing the complex flow of nitrogen through crops in a real-world agricultural setting and describe how experimental metabolomics data, such as isotope labeling rates and analyses of nutrient uptake, can be used to refine these models. In summary, the metabolomics/computational approach offers an exciting mechanism for understanding NUE that may ultimately lead to more effective crop management and engineered plants with higher yields.

Keywords: N boundary; flux balance analysis (FBA); mass spectrometry (MS); metabolomics; nitrogen; nitrogen uptake efficiency (NUpE); nitrogen use efficiency (NUE); nitrogen utilization efficiency (NUtE); nuclear magnetic resonance (NMR); transgenic crops.

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Conflict of interest statement

The authors declare no conflict of interest. The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.

Figures

Figure 1
Figure 1
Multi-dimensional 1H-13C NMR spectrum of aqueous extracts from Medicago sativa seedlings illustrating a typical complement of metabolites observed in untargeted NMR.
Figure 2
Figure 2
15N enrichment levels of two amino acids in barley leaves provided with 15N-labelled KNO3, as determined by gas chromatography-mass spectrometry (GC-MS). Light periods are marked in white and dark periods in gray. Adapted with permission from [78].
Figure 3
Figure 3
Example of a simple metabolic flux model and the equations for defining a flux balance analysis to maximize flux through reaction 5.
Figure 4
Figure 4
A simplified model of boundary fluxes in nitrogen use of crop plants. NUE: Nitrogen use efficiency, NUpE: Nitrogen uptake efficiency, NUtE: Nitrogen utilization efficiency.
See this image and copyright information in PMC

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