Figure 1.

Dissecting pathways regulating the general stress response in five conditions

1. The transcription factors Msn2/4 are the main regulators of the induced branch of yeast general stress response. Msn2/4 are regulated by multiple pathways that respond to a large range of environmental conditions. The motivation for this work was to systematically dissect the contribution of the pathways to the general stress response and reconstruct the regulatory network upstream to Msn2/4.
2. Experimental design. Strains containing genetic perturbations and genomically integrated HSP12-GFP reporter were stimulated. The GFP levels of each strain were measured in 2–3 repeats using flow cytometry under three stress and two growth conditions (Materials and Methods).
3. Examples of target gene deletions that affect the levels of Hsp12-GFP under various stress conditions. The median levels of Hsp12-GFP relative to WT are presented. The knockouts can increase/decrease the GFP levels significantly and this effect can be general or stress specific.
4. The median levels of Hsp12-GFP in 68 mutant strains under five conditions, shown relative to the matching WT levels (log ratio, note color scale; Δ marks are omitted for succinctness). The rows and the columns are clustered hierarchically. The clustering highlights the strong activators/repressors of HSP12-GFP and highlights groups with condition-specific effects.
5. Knockouts were classified according to their condition specificity (Materials and Methods). (left) Venn diagram showing the specificity/commonality of knockouts to stress conditions. (right) Venn diagram comparing stress-dependent effects (in one or more stress conditions) to growth effects.