Figure 2. Expression kinetics of stress-related mRNAs and sRNAs.

Relative changes of mRNAs upon singlet oxygen (¹O₂) stress were monitored by microarray analysis of total RNA at time-points 7, 45, and 90 min and depicted as log₂ ratios. (A) All mRNAs with significant induction (log₂ ratio ≥0.8 and p-value <0.05) at one of the three time-points were applied to clustering using MeV (Multi Experiment Viewer version 4.7.4) from the TM4 Microarray Software Suite [67], [68]. Clustering was based on k-means (KMC method) according to Euclidean distance with a maximum of 50 iterations. Changes were illustrated as heat-maps with a color code ranging from −0.5 (green) to 1.5 (red) log₂ ratio. Columns represent time-points of the stress response and rows represent individual genes. (B–F) Up-regulated mRNAs shown in (A) were grouped together according to their function. Expression kinetics, representing the mean of log₂ ratios, were calculated for functional groups of cluster 1 (B), cluster 2a (C), cluster 2b (D), cluster 2c (E), and cluster 3 (F). (G) Analysis of stress-induced sRNAs. Total RNA was isolated at the indicated time-points and applied to Northern blot analysis. RSs0019, RSs0680a, and RSs0827 were hybridized to radioactively labeled oligonucleotides and visualized by phosphoimaging. 5S rRNA was probed as a control for equal loading of samples (not shown). (H) Genes with described RpoE- and RpoH2-dependent promoters [28], [29], [72] were analyzed when they exhibited log₂ ratios ≥0.8. The curves represent the mean of log₂ ratios based on 12 mRNAs (RpoE, black line) and 42 mRNAs (RpoH2, red line). See supplementary Tables S1 and S2 for further information on regulated genes and their particular functions.