Insights into the genomic nitrate response using genetics and the Sungear Software System

Abstract

Nitrate is both a nutrient and a potent signal that stimulates plant growth. Initial experiments in the late 1950s showing that nitrate enhances nitrate reductase (NR) activity after several hours of treatment have now progressed to transcriptome studies identifying over 1000 genes that respond to muM levels of nitrate within minutes. The use of an Arabidopsis NR-null mutant allowed the identification of genes that respond to nitrate when the production of downstream metabolites of nitrate is blocked. Further dissection of the nitrate response is now possible using new bioinformatic tools such as Sungear to perform comparative studies of multiple transcriptome responses across different laboratories and environmental conditions. These analyses have identified genes and pathways (e.g. nitrate assimilation, pentose phosphate pathway, and glycolysis) that respond to nitrate under a variety of conditions (context-independent). Most of these genes and pathways are ones that were identified using the NR-null mutant as responding directly to nitrate. By contrast, other processes such as protein synthesis respond only under a subset of conditions (context-dependent). Data from the NR-null mutant suggest these latter processes may be regulated by downstream nitrogen metabolites.

Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response ofArabidopsis thalianaroots

“…Sungear allows for the visualization and analysis of multiple datasets to identify genes that are unique or are shared by different gene lists (18,20). We used Sungear to generate a triangle representing the 445 genes with significant T, G, or TG factors (Fig.…”

Improving Nitrogen Use Efficiency in Crops for Sustainable Agriculture

“…Such proteins include those directly involved in N metabolism or those positioned at the interface between C and N metabolism during plant growth and development [150,191,192]. It will be necessary therefore to identify new N-responsive genes through detailed analyses of transcriptomic data sets [189], including using systems biology approaches [109].…”

“…The analyses will be targeted specifically to N uptake, assimilation and recycling in vegetative [165 and reproductive organs [193] at various stages of plant development, using plants grown under different levels of N fertilization. Systems biology consists in taking advantage of various 'omics' data sets including transcriptomics, proteomics and metabolomics that can be further analysed in an integrated manner through the utilization of various mathematical, bioinformatic and computational tools [192]. Ultimately, such integrated analyses may allow the identification of the key individual or common regulatory elements involved in the control of a given biological process [157].…”

The Arabidopsis NRG2 Protein Mediates Nitrate Signaling and Interacts with and Regulates Key Nitrate Regulators

“…Among these genes, those involved in nitrate transport and assimilation, such as several members of the NITRATE TRANSPORT (NRT) gene families and the genes for nitrate and nitrite reductase (NIA and NiR, respectively), are quickly induced (Bi et al, 2007;Wang et al, 2007). In addition, some genes required for controlling carbon metabolism and for providing chemical energy used in reduction and assimilation are induced as well (Price et al, 2004;Scheible et al, 2004;Wang et al, 2004Wang et al, , 2007Fritz et al, 2006;Gutiérrez et al, 2007). Nitrate signaling also influences root growth, development and architecture, seed dormancy, and leaf expansion (Walch-Liu et al, 2000Forde, 2002;Alboresi et al, 2005;Bi et al, 2007;Forde and Walch-Liu, 2009).…”