Available online at www.sciencedirect.com Nitrate signaling: adaptation to fluctuating environments Gabriel Krouk 1,2 , Nigel M Crawford 3 , Gloria M Coruzzi 1 and Yi-Fang Tsay 4 Nitrate (NO 3  ) is a key nutrient as well as a signaling molecule that impacts both metabolism and development of plants. Understanding the complexity of the regulatory networks that control nitrate uptake, metabolism, and associated responses has the potential to provide solutions that address the major issues of nitrate pollution and toxicity that threaten agricultural and ecological sustainability and human health. Recently, major advances have been made in cataloguing the nitrate transcriptome and in identifying key components that mediate nitrate signaling. In this perspective, we describe the genes involved in nitrate regulation and how they influence nitrate transport and assimilation, and we discuss the role of systems biology approaches in elucidating the gene networks involved in NO 3  signaling adaptation to fluctuating environments. Addresses 1 Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, NY 10003, USA 2 Institut de Biologie Inte ´ grative des Plantes, UMR 5004, Biochimie et Physiologie Mole ´ culaire des Plantes, Agro-M/CNRS/INRA/SupAgro/ UM2, 34060 Montpellier cedex 1, France 3 Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA 4 Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan Corresponding author: Krouk, Gabriel (gk40@nyu.edu) and Tsay, Yi-Fang (yftsay@gate.sinica.edu.tw) Current Opinion in Plant Biology 2010, 13:266–273 This review comes from a themed issue on Physiology and metabolism Edited by Uwe Sonnewald and Wolf B. Frommer Available online 21st January 2010 1369-5266/$ – see front matter Published by Elsevier Ltd. DOI 10.1016/j.pbi.2009.12.003 Introduction Reduced forms of nitrogen (NH 4 + , amino acid, peptides, urea...) are poorly available in soils. Conversely, NO 3  is the main source of inorganic nitrogen for plants in aerobic soil conditions. Because of its mobility, partly due to the negative charge of clay, the NO 3  ion concentration can fluctuate in the solution by four orders of magnitude [1], and has consequently become a predominant water pol- lutant. Thus, as sessile organisms, plants have evolved at least 3 adaptation processes to tackle this environmental constraint. First, plants tune their transport activity to the NO 3  availability [2  ]. Second, plants can store NO 3  in vacuoles to remobilize it [3]. Third, the adaptation of root architecture to nitrogen availability in the soil is a classic example of a plant developmental adaptation to its environment. In fact, this year marks the 11th anniversary of the identification of the MADS-box Transcription Factor (TF) ANR1 that has been implicated in the control of lateral root development (LRD) in response to loca- lized nitrate supply [4]. Despite this early major advance, very few studies since have identified regulatory proteins controlling NO 3  responses. A more extensively studied event is the ‘NO 3  primary response’, which is charac- terized by a strong and rapid transcriptional induction of nitrate-responsive genes including those involved in NO 3  transport (e.g. NRT1.1, NRT2.1), [5–8]) or NO 3  assimilation (e.g. NIR, or NIA1). It is only very recently that the regulatory networks that mediate the NO 3  response have begun to reveal their secrets. This review puts in context the recent findings of the new molecular actors controlling NO 3  transport and signaling from a molecular physiology point of view to a system scale. Overview of nitrate transport, assimilation and regulation Nitrate is assimilated via a regulated network of transpor- ters (Figure 1), reductases, synthetases, and transaminases that respond to internal and environmental signals that integrate nitrate assimilation with carbon (C) and energy metabolism [2,9–12]. Key signals include nitrate [5,7], light [13], sucrose [14,15], and metabolites of the pentose phos- phate pathway [16  ,17]. Nitrate assimilation also responds to circadian rhythms [18] and long distance signals [19,20], which have been proposed to include amino acids such as glutamine (Gln) [21] and the phytohormone auxin [22]. These signals not only ensure that sufficient C and energy are available for the assimilation of inorganic nitrogen, but also regulate root development and architecture to control N uptake in roots. Responses to these signals occur at multiple levels including transcriptional and post-transla- tional [12]. Nitrate elicits rapid changes in gene expression for about 10% of the detectable transcriptome, with specific genes responding within 5–10 min of submicro- molar concentrations of nitrate or nitrite [6,8,23]. N-depri- vation also elicits a strong transcriptional response [8,24,25]. C and light signaling interface with N regulation and serve to enhance N responses [26,27]. Some of these transcriptional responses correlate with changes at the protein level, as observed in proteomic analysis [28  ]. At the post-translational level, phosphorylation has been the primary mechanism documented to date. Rapid and reversible phosphorylation of nitrate reductase occurs in response to dark or anoxia, which renders the enzyme receptive to inhibition by binding of 14-3-3 proteins Current Opinion in Plant Biology 2010, 13:266–273 www.sciencedirect.com