An extreme example of eutrophication of the Potomac River, US, evident from its bright green water, caused by a dense bloom of cyanobacteria. Eutrophication is an increase in chemical nutrients in an ecosystem. Developing ways to increase nitrogen use efficiency in plants could reduce fertiliser cost and nitrogen pollution Photo: US National Oceanic and Atmospheric Administration/Wikipedia

An international team of researchers, using a systems biological analysis of genome-scale data from Arabidopsis plants, have identified that the master gene controlling the biological clock is sensitive to nutrient status. The research has outlined how nutrients affect the molecular networks controlling plant growth and development in response to nutrient sensing.

The team was made up of researchers from New York University’s Centre for Genomics and Systems Biology, Chile’s Pontificia Universidad Catolica de Chile, Dartmouth College and Cold Spring Harbour Labs. The team discovered that the systems biology approach to uncovering nutrient regulated gene networks provides new targets for engineering traits in plant and agronomic interest such as increased nitrogen use efficiency, which could reduce fertiliser cost and nitrogen pollution.

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Nitrate has been shown to serve as a signal for the control of the gene expression in Arabidopsis, the first plant with its entire genome sequenced. The study indicates that, on a gene by gene basis, the products of nitrogen assimilation such as amino acid glutamate (Glu) or glutamine (Gln), might serve as signals of organic nitrogen status that are sensed, and resultantly, regulate gene expression.

To identify responses to organic nitrogen signals, the team treated Arabidopsis seedlings with inorganic nitrogen in both the presence and absence of chemicals that inhibit the assimilation into organic nitrogen and conducted a genome-wide analysis of all genes whose expression responds to either, inorganic or organic, forms of nitrogen. 

They found that by using an integrated network model of molecular interactions for the plant, where roughly 7000 genes are connected by 230,000 molecular interactions, they uncovered a sub-network of genes regulated by organic nitrogen, including a highly connected network “hub” CCA1, which controlled the plant’s biological clock, and targeted genes involved in nitrogen assimilation.  

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