Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress

Abstract

To identify genes of potential importance to cold, salt, and drought tolerance, global expression profiling was performed on Arabidopsis plants subjected to stress treatments of 4 degrees C, 100 mM NaCl, or 200 mM mannitol, respectively. RNA samples were collected separately from leaves and roots after 3- and 27-h stress treatments. Profiling was conducted with a GeneChip microarray with probe sets for approximately 8,100 genes. Combined results from all three stresses identified 2,409 genes with a greater than 2-fold change over control. This suggests that about 30% of the transcriptome is sensitive to regulation by common stress conditions. The majority of changes were stimulus specific. At the 3-h time point, less than 5% (118 genes) of the changes were observed as shared by all three stress responses. By 27 h, the number of shared responses was reduced more than 10-fold (< 0.5%), consistent with a progression toward more stimulus-specific responses. Roots and leaves displayed very different changes. For example, less than 14% of the cold-specific changes were shared between root and leaves at both 3 and 27 h. The gene with the largest induction under all three stress treatments was At5g52310 (LTI/COR78), with induction levels in roots greater than 250-fold for cold, 40-fold for mannitol, and 57-fold for NaCl. A stress response was observed for 306 (68%) of the known circadian controlled genes, supporting the hypothesis that an important function of the circadian clock is to "anticipate" predictable stresses such as cold nights. Although these results identify hundreds of potentially important transcriptome changes, the biochemical functions of many stress-regulated genes remain unknown.

Figure 1

Venn diagrams showing an overview of stress-regulated changes (> 2-fold) for different treatment conditions. Stress-induced changes were identified in 2,678 probe sets (which approximately equals the number of genes). The number of changes and the percentage corresponding to up-regulation are shown. Numbers for fresh medium represent a comparison between 3 and 27 h. Numbers for the three stresses represent a comparison with the average of the 3- and 27-h control.

Figure 2

Venn diagrams showing the distribution of stimulus-specific and shared stress responses (> 2-fold). Numbers in italics correspond to probe sets identified in a specific category. Most of these changes were only observed once as a transient change. Non-italicized numbers in parentheses correspond to individual genes that passed a more stringent criterion for reproducibility (see text). Further information on these selected changes can be found in Tables II through V (shown here) or as supplemental information in Supplemental Tables 2A–G and 3A–G (They can be viewed at www.plantphysiol.org).