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Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana

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Abstract Nitrogen (N) is an essential macronutrient for plants. In nature, N cycles between different inorganic and organic forms some of which can serve as nutrients for plants. The inorganic N forms nitrate and ammonium are the most important sources of N for plants. However, plants can also uptake and use organic N forms such as amino acids and urea. Besides their nutritional role, nitrate and other forms of N can also act as signals that regulate the expression of hundreds of genes causing modulation of plant metabolism, physiology, growth, and development. Although many genes and processes affected by changes in external or internal N have been identified, the molecular mechanisms involved in N sensing and signaling are still poorly understood. Classic reverse and forward genetics and more recently the advent of genomic and systems approaches have helped to characterize some of the components of the signaling pathways directing Arabidopsis responses to N. Here, we provide an update on recent advances to identify the components involved in N sensing and signaling in Arabidopsis and their importance for the plant response to N. Copyright © 2010 John Wiley & Sons, Inc. This article is categorized under: Biological Mechanisms > Cell Signaling

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Recent advances in identifying the molecular pathways controlling Arabidopsis responses to N. Green circles represent transcription factors, blue circles represent enzymes, and yellow triangles represent miRNAs. Black lines represent the relationships inferred by genetic approaches, red lines represent the relationships inferred by systems biology approaches, and blue lines represent the relationships inferred by both genetic and systems biology approaches. (A) High nitrate situation: nitrate is transported and sensed by the NRT1.1 transporter. Inside the cell, nitrate can regulate nitrate primary response genes such as NIA, NiR, and NRT2.1 and primary root growth by a pathway involving calcium accumulation, the calcineurin B‐like (CBL) proteins and the CIPK8 protein kinase12 or the NLP7 transcription factor21 (a and b). Nitrate can also interact with the cytokinin, abscisic acid (ABA), and/or auxin signaling pathways to regulate developmental programs and protein synthesis22–26 (c), repress seed dormancy27 (d), and repress lateral root growth28–30 (e). Localized high nitrate supply is also known to induce the MADS‐box transcription factor ANR1 to promote lateral root elongation9,15 (f). N metabolites produced by nitrate reduction and assimilation also have signaling roles repressing lateral root growth by a pathway involving ANR116 (g), determining the ratio between initiating and elongating lateral roots by regulation of the miR167/ARF8 module in the pericycle6 (h), regulating Gln biosynthesis by regulation of the ASN1, GDH1, and GLN1.3 genes by the master clock gene CCA131 (i), and repressing primary root growth4,17,18 (j). Nitrate is also able to alleviate primary root growth inhibition by glutamate (k). (B) Low nitrate situation: nitrate can be transported and probably sensed by the high‐affinity NRT2.1 transporter. Limiting nitrate conditions can regulate drought tolerance by repressing miR169 and inducing the A5 subunit of the NF‐Y transcription factor32 (l), regulate the expression of genes related to N stress adaptation by pathways involving NLP7 and NLA21,33–35 (m and n), and induce lateral root initiation when plants are transferred from high to low nitrate conditions5 (o). See the text for more details.

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Regulatory networks for N responses in Arabidopsis. Nitrate and other N sources produced by nitrate reduction by the nitrate assimilatory pathway are able to act as signals that regulate molecular processes and pathways (purple rounded rectangles), leading to regulation of developmental processes (green rounded rectangles). The arrow heads or lines at the end of the edges indicate the direction of information or metabolic flow. 2‐OG, 2‐oxoglutarate; ABA, abscisic acid; ASN1, asparagine synthetase 1; CCA1, circadian clock associated 1; CK, cytokinin; GDH1, glutamate dehydrogenase 1; GLN1, glutamine synthetase 1; GOGAT, glutamate synthase; IPT3, isopentenyl transferase 3; NIA, nitrate reductase; NiR, nitrite reductase; and NRT, nitrate transporter. See the text for more details.

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