Figure 5. RNA-sequencing reveals cellular functions that are regulated during glucose and the lag phase.

(A) Experimental set-up of the RNA-Seq experiment. The wild-type strain adapted to maltose growth was transferred to glucose for different times (0, 2, 4, 6, 8, 10, 12 hr) before switching it back to maltose. Multiple samples (indicated by stars) were taken during the different growth phases. The final sample was taken when the cultures increased 4-fold after the shift to maltose. (B) Heatmap representing a selection of non-redundant GO categories that were significantly enriched in the set of up- or downregulated genes of at least three samples throughout the experiment (Materials and Methods). The heatmap displays the GO category on the horizontal axis, the sample on the vertical axis, while the color scale indicates enrichment of the GO category. The clustering by rows reveals groups of related GO categories which are indicated on the right in grey boxes.

Figure 5—figure supplement 1. Detection of genes that show large transcriptional changes between 1 hr and 12 hr after the shift to glucose.

The slope of log2 gene expression changes versus time during glucose is plotted against the mean of these changes. All expression changes are relative to the initial sample taken during growth on maltose. Highlighted are upregulated genes with gradually increasing or decreasing expression levels during glucose (orange and brown respectively), and downregulated genes with gradually increasing or decreasing expression levels during glucose (green and blue respectively).

Figure 5—figure supplement 2. Log2 expression changes during glucose growth for the genes that show large transcriptional changes between 1 hr and 12 hr after the shift to glucose Log2 expression of the genes highlighted in Figure 5—figure supplement 1 is shown between 1 hr and 12 hr after the shift to glucose.

The color codes are the same as in Figure 5—figure supplement 1.

Figure 5—figure supplement 3. Correlation between the lag behavior upon gene deletion (Bar-Seq), and the expression change of the corresponding genes during glucose growth (RNA-Seq).

The vertical axis shows the lag time and the horizontal axis shows the expression change during glucose growth. Both measures in the two axes show the results from the samples that have been growing in glucose for 12 hr. The four types of gene deletion mutants shown in Figure 4A are highlighted (short = blue; long = red; long-then-short=green; short-then-long=purple).

Figure 5—figure supplement 4. Correlation between protein and mRNA level changes during glucose growth after pre-growth on maltose.

The protein levels are measured using flow cytometry in strains with fluorescent protein fusion constructs. The mRNA is quantified as the number of transcripts mapped to the target gene per one million reads (TPM). Cells are pre-grown in maltose media and afterwards shifted to glucose. At the shown time points in glucose the ratio of protein (or mRNA) level to the level at the end of maltose pre-growth is calculated.