Perturbation of lipid metabolism leads to derepression of stress genes.

(A) Heatmap of gene expression in WT, cbf11Δ, and cbf12Δ cells upon treatment with 0.74 mM H₂O₂ in YES medium. Transcript levels were determined by a timecourse microarray analysis and normalized to untreated WT values. Only genes showing ≥2-fold change in expression in at least one condition are shown. This experiment was performed once. (B) Distribution of all relative transcript levels in WT cells treated for 60 min with H₂O₂ and untreated cbf11Δ cells from the experiment in panel A. Values represent log2 of fold-changes in expression compared to untreated WT. Individual genes are shown as dots; blue and yellow dots represent ≥2-fold down- and upregulated genes, respectively. The 10 genes downregulated in untreated cbf11Δ cells are highlighted with a red circle. (C) Biological functions of the 10 genes downregulated in untreated cbf11Δ cells from panel B were determined using slimmed Gene Ontology Biological Process annotations [35]. Known direct Cbf11 targets are in bold. (D) Expression of the indicated stress genes in untreated WT, cbf11DBM-TAP, mga2Δ, Pcut6MUT, and cut6-621 cells growing in YES was analyzed by RT-qPCR. The temperature sensitive cut6-621 mutant was shifted to a semi-restrictive temperature to inhibit Cut6 function prior to analysis. Mean and SD values of three independent replicates are shown. One-sided Mann-Whitney U test was used to determine statistical significance. (E) Survival and growth under oxidative stress of WT, cbf11Δ, cbf11DBM-TAP, mga2Δ, Pcut6MUT, and cut6-621 cultures spotted on YES plates containing 2 mM H₂O₂. The plates were incubated at 32°C, which is a semi-restrictive temperature for the cut6-621 mutant. (F) Expression of the indicated stress genes in WT cells treated with DMSO (control) or 20 μM cerulenin for 1 hour in YES was analyzed by RT-qPCR. Mean and SD values of two independent replicates are shown.