Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis

Abstract

Background: A large quantity of nitrogen (N) fertilizer is used for crop production to achieve high yields at a significant economic and environmental cost. Efforts have been directed to understanding the molecular basis of plant responses to N and identifying N-responsive genes in order to manipulate their expression, thus enabling plants to use N more efficiently. No studies have yet delineated these responses at the transcriptional level when plants are grown under chronic N stress and the understanding of regulatory elements involved in N response is very limited.

Results: To further our understanding of the response of plants to varying N levels, a growth system was developed where N was the growth-limiting factor. An Arabidopsis whole genome microarray was used to evaluate global gene expression under different N conditions. Differentially expressed genes under mild or severe chronic N stress were identified. Mild N stress triggered only a small set of genes significantly different at the transcriptional level, which are largely involved in various stress responses. Plant responses were much more pronounced under severe N stress, involving a large number of genes in many different biological processes. Differentially expressed genes were also identified in response to short- and long-term N availability increases. Putative N regulatory elements were determined along with several previously known motifs involved in the responses to N and carbon availability as well as plant stress.

Conclusion: Differentially expressed genes identified provide additional insights into the coordination of the complex N responses of plants and the components of the N response mechanism. Putative N regulatory elements were identified to reveal possible new components of the regulatory network for plant N responses. A better understanding of the complex regulatory network for plant N responses will help lead to strategies to improve N use efficiency.

Figure 1

Three-week-old wild type Arabidopsis plants under different N conditions. A: Shoot biomass. Average of shoot biomass (mg/plant) of 6 to 8 three-week-old wild type Arabidopsis plants under the N-sufficient (3 mM), mild (1 mM) and severe (0.3 mM) N-limiting conditions are presented, as well as sd. B: Nitrate levels: Average of nitrate levels (mg/g fresh weight) of 3 biological samples under different N conditions (each sample from a pool of 3 plants) are presented, as well as sd.

Figure 2

Expression patterns of genes in each cluster. Relative expression levels of genes in each cluster were presented. The warmer the colors are, the higher the expression levels are. 3 mM = the sufficient-N condition; 1 mM = the limiting-N condition; 0.3 mM = the stress-N condition; 2 hr = 2 hr induction; 24 hr = 24 hr induction. Each line represents one gene and the gene list is provided in Additional file 7.