Systems Biology for Enhanced Plant Nitrogen Nutrition

FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago, Chile.
Science (Impact Factor: 33.61). 06/2012; 336(6089):1673-5. DOI: 10.1126/science.1217620
Source: PubMed


Nitrogen (N)-based fertilizers increase agricultural productivity but have detrimental effects on the environment and human health. Research is generating improved understanding of the signaling components plants use to sense N and regulate metabolism, physiology, and growth and development. However, we still need to integrate these regulatory factors into signal transduction pathways and connect them to downstream response pathways. Systems biology approaches facilitate identification of new components and N-regulatory networks linked to other plant processes. A holistic view of plant N nutrition should open avenues to translate this knowledge into effective strategies to improve N-use efficiency and enhance crop production systems for more sustainable agricultural practices.

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Available from: Rodrigo A Gutierrez, Jan 21, 2014
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    • "Thus, to satisfy the growing global population's increasing demands for food, raw materials and biofuels, large amounts of N fertilizer (∼120 Tg N year −1 ) are applied to agricultural soils ( Robertson and Vitousek 2009). However, up to 75% of the N fertilizer applied is not absorbed by plants and it is lost to the environment, thereby leading to the eutrophication of water and enrichment of NO x gases in the atmosphere ( Gutierrez 2012). To sustain high productivity and decrease the rate of N application, it is important to obtain a better understanding of the molecular regulatory mechanisms underlying morphological and physiological acclimation to N availability in crops ( Rennenberg et al. 2010, Xu et al. 2012). "
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    ABSTRACT: Nitrogen (N) starvation and excess have distinct effects on N uptake and metabolism in poplars, but the global transcriptomic changes underlying morphological and physiological acclimation to altered N availability are unknown. We found that N starvation stimulated the fine root length and surface area by 54 and 49%, respectively, decreased the net photosynthetic rate by 15% and reduced the concentrations of NH 4 + , NH4+, NO 3 − NO3− and total free amino acids in the roots and leaves of Populus simonii Carr. in comparison with normal N supply, whereas N excess had the opposite effect in most cases. Global transcriptome analysis of roots and leaves elucidated the specific molecular responses to N starvation and excess. Under N starvation and excess, gene ontology (GO) terms related to ion transport and response to auxin stimulus were enriched in roots, whereas the GO term for response to abscisic acid stimulus was overrepresented in leaves. Common GO terms for all N treatments in roots and leaves were related to development, N metabolism, response to stress and hormone stimulus. Approximately 30–40% of the differentially expressed genes formed a transcriptomic regulatory network under each condition. These results suggest that global transcriptomic reprogramming plays a key role in the morphological and physiological acclimation of poplar roots and leaves to N starvation and excess.
    Full-text · Article · Sep 2015 · Tree Physiology
    • "Recently, a number of genes have been identified that control root morphological changes in response to N availability. These include genes that function in nitrate and ammonium transport, nitrate sensing, and the biosynthesis and signaling of plant hormones (Gutiérrez, 2012; Forde, 2014; Ma et al., 2014). These advances may facilitate the development of N-efficient crops through transgenic approaches that target root architecture and root responses to N availability . "
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    ABSTRACT: Nitrate is a major nitrogen resource for cereal crops, thus understanding nitrate signaling in cereal crops is valuable for engineering crops with improved nitrogen use efficiency. Although several regulators have been identified in nitrate sensing and signaling in Arabidopsis, the equivalent information in cereals is missing. Here, we isolated a nitrate-inducible and cereal-specific NAC transcription factor TaNAC2-5A from wheat (Triticum aestivum). Chromatin immunoprecipitation (ChIP) assay showed that TaNAC2-5A could directly bind to the promoter regions of the genes encoding nitrate transporter and glutamine synthetase. Overexpression of TaNAC2-5A in wheat enhanced root growth and nitrate influx rate, and hence increase root ability to acquire nitrogen. Further, we found that TaNAC2-5A-overexpressing transgenic wheat lines had higher grain yield and higher nitrogen accumulation in aerial parts, and allocated more nitrogen in grains in a field experiment. These results suggest that TaNAC2-5A is involved in nitrate signaling, and show that it is an exciting gene resource for breeding crops with more efficient use of fertilizer.
    No preview · Article · Sep 2015 · Plant physiology
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    • "In contrast, lateral roots elongate for N foraging when they locally receive an adequate amount of NO 3 (Zhang and Forde 1998; Remans et al. 2006a). The function of the NPF6.3 nitrate/auxin transporter and the action of its downstream networks further corroborate the roles of NO 3 -dependent signals associated with the development of lateral roots following transfer of plants from N-deprived to N-replete conditions (Vidal et al. 2010; Gutiérrez 2012; Vidal et al. 2013; Bouguyon et al. 2015; Giehl and von Wirén 2015). Besides these morphological responses to NO 3 supply , plant roots display different architectures in the presence of alternative N sources. "
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    ABSTRACT: Plant root development is strongly affected by nutrient availability. Despite the importance of structure and function of roots in nutrient acquisition, statistical modeling approaches to evaluate dynamic and temporal modulations of root system architecture in response to nutrient availability have remained widely open and exploratory areas in root biology. In this study, we developed a statistical modeling approach to investigate modulations of root system architecture in response to nitrogen availability. Mathematical models were designed for quantitative assessment of root growth and root branching phenotypes and their dynamic relationships based on hierarchical configuration of primary and lateral roots formulating the fishbone-shaped root system architecture in Arabidopsis thaliana. Time-series datasets reporting dynamic changes in root developmental traits on different nitrate or ammonium concentrations were generated for statistical analyses. Regression analyses unraveled key parameters associated with (i) inhibition of primary root growth under nitrogen limitation or on ammonium, (ii) rapid progression of lateral root emergence in response to ammonium, and (iii) inhibition of lateral root elongation in the presence of excess nitrate or ammonium. This study provides a statistical framework for interpreting dynamic modulation of root system architecture, supported by meta-analysis of datasets displaying morphological responses of roots to diverse nitrogen supplies.
    Full-text · Article · Sep 2015 · Journal of Integrative Plant Biology
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