Nitrate in 2020: Thirty Years from Transport to Signaling Networks

Abstract

Nitrogen (N) is an essential macronutrient for plants and a major limiting factor for plant growth and crop production. Nitrate is the main source of N available to plants in agricultural soils and in many natural environments. Sustaining agricultural productivity is of paramount importance in the current scenario of increasing world population, diversification of crop uses, and climate change. Plant productivity for major crops around the world, however, is still supported by excess application of N-rich fertilizers with detrimental economic and environmental impacts. Thus, understanding how plants regulate nitrate uptake and metabolism is key for developing new crops with enhanced N use efficiency and to cope with future world food demands. The study of plant responses to nitrate has gained considerable interest over the last 30 years. This review provides an overview of key findings in nitrate research, spanning biochemistry, molecular genetics, genomics, and systems biology. We discuss how we have reached our current view of nitrate transport, local and systemic nitrate sensing/signaling, and the regulatory networks underlying nitrate-controlled outputs in plants. We hope this summary will serve not only as a timeline and information repository but also as a baseline to define outstanding questions for future research.

Figure 1.

A Timeline with Milestone Publications in Nitrate Signaling. The terms “nitrate” and “Arabidopsis” were used to retrieve articles and their citation numbers from Web of Science (http://www.webofknowledge.com). We selected articles specifically focused on nitrate signaling or acquisition in this timeline (listed in Supplemental Data Set 2), based on the number of citations. Three additional articles related to early studies in crops (1950s to 1980s) were included. Please note that the sizes of circles are proportional to the number of citations normalized by years from publication. Top articles related to nitrate signaling were included for this timeline.

Figure 2.

A Summary of Nitrate Signaling Pathways. NRT1.1 is at the first layer of the nitrate signaling pathway. CIPK23, CBL1/9, and ABI2 control the NRT1.1 phosphorylation status, switching its nitrate affinity. The transduced nitrate signal through NRT1.1 activates PLC activity, increasing calcium accumulation. Then, the calcium signals are decoded by subgroup III CPKs, which in turn phosphorylate the NLP7 transcription factor, promoting its nuclear retention and the activation of nitrate-responsive target genes. NLP7 physically interacts with NLP6, TCP20, and NRG2 to activate the expression of genes involved in nitrate metabolism. NRT2.1 has also been proposed as a nitrate sensor. Myriad TFs have been discovered as important regulators of gene expression in response to nitrate or as integrators of N and P signaling (HRS1, HHO1, and PHR1). See text and Supplemental Data Set 2 for relevant references.

Figure 3.

Integrative GRN Analysis with the Most Influential TFs in N-Regulatory Networks. Genes are drawn as pentagons (transcription factors) or circles (target genes). The size of the triangle is proportional to the number of targets bound or regulated by each TF (outdegree). The four TF layers were organized according to their outdegree. TFs were selected based on published evidence of TF regulation or TF binding to genes involved in N transport, N reduction, and N assimilation in Arabidopsis. Blue edges indicate ChIP binding data (Gutiérrez et al., 2008; Marchive et al., 2013; Alvarez et al., 2014; Guan et al., 2014; Para et al., 2014). Orange edges indicate TARGET and Y1H data (Para et al., 2014; Medici et al., 2015; Gaudinier et al., 2018; Varala et al., 2018; Brooks et al., 2019). Red edges indicate in planta TF regulation and chromatin accessibility (Gutiérrez et al., 2008; Rubin et al., 2009; Marchive et al., 2013; Xu et al., 2016b; Maeda et al., 2018; Alvarez et al., 2019; Brooks et al., 2019). The pink border of the pentagons denotes TF regulated in response to nitrate (Alvarez et al., 2019).