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Accumulation of NLP7-GFP in the nuclei of A. thaliana root cells after adding nitrate. Observation under confocal microscope.. © INRA, Chloé Marchive

Discovery of a crucial factor in the adaptation of plants to nitrogen availability

Nitrogen is an essential element in plant growth, but its availability in the soil – in a nitrate form – may vary, which brings into play specific regulatory mechanisms in the plant designed to coordinate its transport and assimilation.  Scientists from INRA in Versailles-Grignon, and ENS-Paris (1) have demonstrated the crucial role of a transcription factor, NLP7, in the early response of plants to nitrate via a nuclear retention mechanism.  The results of their work were published on 16 April 2013 in the journal Nature Communications.

Updated on 07/05/2017
Published on 04/16/2013

Maintaining crop yields while reducing nitrate inputs into fields is a challenge that requires a clearer understanding of how plants respond to nitrogen supplementation.  Researchers at INRA in Versailles-Grignon and their colleagues from ENS-Paris have focused on the role of a transcription factor (2), NLP7, in the signalling pathway for nitrates - the principal source of nitrogen – in the model plant Arabidopsis thaliana (thale cress) when it grows in our gardens.

NLP7, a transcription factor that is crucial to the response of plants to nitrogen availability

Accumulation of NLP7-GFP in the nuclei of A. thaliana root cells after adding nitrate. Observation under confocal microscope.. © INRA, Chloé Marchive
Accumulation of NLP7-GFP in the nuclei of A. thaliana root cells after adding nitrate. Observation under confocal microscope. © INRA, Chloé Marchive
By combining imaging and genomic techniques, the scientists demonstrated that as a function of the amount of nitrate available, the NLP7 transcription factor was not always located in the same compartment of plant cells (nucleus, cytoplasm), which thus influenced its activity.  When nitrate was available in sufficient quantities for the plant, NLP7 was present in cell nuclei, but it was exported into the cytoplasm in the case of nitrate deficiency.

They then showed that NLP7 binds to more than 800 genes, a large number of which are involved in the nitrate signalling and assimilation pathways.  The broad range of NLP7 target genes thus testifies to its important role in plant responses to nitrate.  Depending on the genes, this binding causes the activation or repression of this response, although this difference may be due to other regulatory factors intervening alongside NLP7.  More specifically, the researchers showed that the nuclear retention of NLP7 occurred very early, within a few minutes of nitrate input, thus suggesting an upstream regulatory role in the plant response to nitrates.

NLP7 may thus trigger implementation of a gene expression programme that allows the plant to transform nitrate into the organic nitrogen (amino acids, etc.) it needs for the synthesis of proteins or nucleic acids, as well as activating growth and the development of new organs.

Two elements of a novel finding

Overall, these results have revealed a hitherto unknown characteristic of plants: localisation of the NLP7 transcription factor is regulated by nitrate via a retention mechanism in cell nuclei, and it is this retention which orchestrates the early and rapid response of plants to nitrates.  This mechanism ensures the rapid adaptation of plants to nitrate availability and among other things permits its rapid absorption from the soil.

Although this to-and-fro mechanism between two cell compartments has already been observed in plants in the context of relationships with pathogenic organisms or signalling pathways that involve light, it is the first time it has been described in the case of a signalling pathway for an essential nutrient.

More generally, although the maintenance of biomass production and grain quality while limiting nitrate fertilisation currently constitutes the principal challenge for modern agriculture, this discovery opens the way to interesting opportunities to improve control of the response of plants to nitrate availability.

(1) Institut Jean-Pierre Bourgin (INRA, AgroParisTech), Institut de Biologie of ENS (IBENS)
(2) Transcription is the first stage in the process of change from DNA to a protein, or in other words from a gene to its product.  It allows the copying of DNA into RNA, which during a second stage is translated into proteins.


Marchive C. et al. Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants. Nat. Commun. 16 April 2013. doi: 10.1038/ncomms2650.

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Nitrogen, an essential element for plant growth

Nitrogen plays an important role in plant metabolism and growth.  It is the principal constituent of proteins and nucleic acids (the substrates for genetic information), and in a multitude of secondary metabolites.

Most plants are incapable of utilising the nitrogen present in air.  It must thus be absorbed, principally in nitrate form, from the soil via the roots.  This inorganic nitrogen is then assimilated to produce organic nitrogen (present in carbon molecules) which will be used to produce proteins and nucleic acids.  Thus the growth and yields of crops are often restricted by soil nitrate availability.  The use of nitrate fertilisers has enabled a considerable increase in crop yields, even though this can sometimes have harmful effects on the environment.

An essential element in crop fertilisation, nitrogen (in nitrate form) also plays an important role as a signal molecule in the expression of a large number of genes, a process for which only a few regulatory elements have been identified to date.  These include the transcription factor (2) NLP7, whose expression is constitutive, or in other words independent of the nitrate level.