Figure 5.

Transcriptome Profiling during Dark-to-Light Transition.

(A) Differences of gene expression levels among various strains in the dark. The bar graph shows the number of consistently differentially expressed genes in 4A+ (versus hmox1, ho1C1, and ho1C2), hmox1 (versus 4A+, ho1C1, and ho1C2), ho1C1 (versus hmox1, 4A+, and ho1C2), and ho1C2 (versus hmox1, ho1C1, and 4A+) at the beginning of the experiment in the dark.

(B) Responses of the transcriptome in hmox1 and control strains during the transition from dark to light. Venn diagrams show the overlap of genes changing during the transition from darkness to 0.5 h in the light (top) and from darkness to 4 h in the light (bottom). The number of genes changing similarly in hmox1, hmox1+BV, ho1C1, and ho1C2 is shown in the central overlap regions in yellow and orange. The number of genes that were consistently changing only in the genetically (ho1C1 or ho1C2) and chemically (hmox1+BV) complemented (comp) strains are shown on the right in pink and red. The numbers of genes found to be consistently different in hmox1 compared with complemented strains are shown on the left in cyan and green.

(C) HMOX1-dependent gene expression. The bar graph shows the number of consistently differentially expressed genes in hmox1 compared with chemically (hmox1+BV) and genetically (ho1C1 or ho1C2) complemented strains in the dark and 0.5 or 4 h after transition into the light. The mRNAs found to be changed at 0.5 and 4 h in the light in hmox1 specifically are found in the central intersection of the Venn diagram underneath the graph, defining the number of differentially accumulating mRNAs common to both 0.5 and 4 h transcriptomes.

(D) Transcript abundance changes of 50 genes consistently different between hmox1 and both genetically and chemically complemented strains, at both 0.5 and 4 h after transition from dark to light. Box color (blue, increase; red, decrease) indicates log₂-transformed fold change of transcript abundances between hmox1 and hmox1+BV, hmox1 and ho1C1, and hmox1 and ho1C2 at 0.5 or 4 h in the light, and transcript abundances between dark acclimated cells and 4 h upon transition into the light (0 → 4 h). Red outlines indicate nonsignificant changes (1% FDR).