Figure 2

Panorama of ER stress response in N. crassa. (A) The pattern of intensity-dependent ER stress response (left: mild stress induced by 0.1 mM DTT or 5 μg/mL TM; right: acute stress induced by 5 mM DTT or 40 μg/mL TM) was plotted by calculating the log₂ normalized fold changes in wild-type cells treated with DTT or TM versus the mock treatment. Each point represents a transcript with a detected expression level. Points filled with light-pink or light-blue represent genes expression with increased or decreased abundance (q value ≥0.95) upon ER stress. Gray points represent genes with no differences in the expression or false positives (see the ‘Materials and methods’ section for detail). Cellulases (red points), hemicellulases (yellow points), and extracellular proteins (dark blue points) previously identified by LC-MS [14] are indicated to show the RESS. The black dotted line represents a manually defined threshold (|log₂ ratio| = 1). The mean of D value (the difference of RPKM for each gene between two samples in each comparison) of two comparisons (DTT and TM) from NOISeq results were plotted and the size of dots reflects a given level of transcript abundance. The locations of eight known UPR targets in the diagram are indicated to demonstrate that UPR was elicited successfully. (B) Four-way Venn diagram pooling genes according to their expression response to the four different treatments. Marked (black bar) are the 766 ESRTs up-regulated by both DTT and TM at either mild or acute ER stress levels (left) and the 759 down-regulated targets upon ER stress (right).