The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast

Abstract

The Ume6 transcription factor in yeast is known to both repress and activate expression of diverse genes during growth and meiotic development. To obtain a more complete profile of the functions regulated by this protein, microarray analysis was used to examine transcription in wild-type and ume6Delta diploids during vegetative growth in glucose and acetate. Two different genetic backgrounds (W303 and SK1) were examined to identify a core set of strain-independent Ume6-regulated genes. Among genes whose expression is controlled by Ume6 in both backgrounds, 82 contain homologies to the Ume6-binding site (URS1) and are expected to be directly regulated by Ume6. The vast majority of those whose functions are known participate in carbon/nitrogen metabolism and/or meiosis. Approximately half of the Ume6 direct targets are induced during meiosis, with most falling into the early meiotic expression class (cluster 4), and a smaller subset in the middle and later classes (clusters 5-7). Based on these data, we propose that Ume6 serves a unique role in diploid cells, coupling metabolic responses to nutritional cues with the initiation and progression of meiosis. Finally, expression patterns in the two genetic backgrounds suggest that SK1 is better adapted to respiration and W303 to fermentation, which may in part account for the more efficient and synchronous sporulation of SK1.

Figure 1

Ume6-regulated genes in SK1. Venn diagram showing the number of genes deregulated during growth of SK1 ume6Δ and W303 ume6Δ in glucose and acetate media. Shaded regions indicate genes containing promoter sequences corresponding to the URS1 hexamer.

Figure 2

Strain-independent Ume6-regulated genes. (A) Venn diagram showing the genes deregulated in each strain during growth in glucose and/or acetate by the 5-fold criteria. This “core” set of Ume6-regulated genes consists of 74 “direct” (URS1-containing) and 143 “indirect” targets deregulated in common in both strains. (B) Histograms indicating the levels of derepression of the core Ume6 direct target genes in glucose and acetate (fluorescence intensities for ume6Δ/UME6). Only one gene, REV1, exhibited increased expression in the ume6 mutant (25-fold in SK1 glucose and 14-fold in W303 glucose; not shown), suggesting it is likely activated rather than repressed by Ume6 during vegetative growth.

Figure 3

Function and expression of Ume6 targets. (A) Functional classifications of the 82 direct Ume6 targets in the core. The indirect core of 143 genes (from the 5-fold criteria) with known functions fall into the following Munich Information Center for Protein Sequences (MIPS) functional classes: energy (19%), metabolism (16%), cell growth/division/DNA synthesis (12%), intracellular transport (9.5%), cell rescue/defense/aging (8.1%), transcription (8.1%), cellular biogenesis (6.8%), protein destination (6.8%), protein synthesis (6.8%), transport facilitation (4%), ionic homeostasis (2.7%) (40). (B) Expression of the 42 meiotically induced core Ume6-regulated genes during growth and meiosis. Red and blue indicate high and low expression levels, respectively. For each strain, columns represent vegetative growth of UME6 and ume6Δ in acetate and glucose (Left) or timepoints during meiosis (Right; ref. 13). The meiotic expression classes of the genes are indicated on the far right. Note that Ime2 exhibits a biphasic induction and therefore has been categorized as both an early and middle gene (13).

Figure 4

URS1 consensus sequence derived from alignment of GGCGGC hexamer sequences in the promoters (+200 to −600 upstream) of the 82 direct core genes. The previously described consensus (3) is in bold, and has been extended to include additional flanking nucleotides present at a frequency (indicated below the consensus) of at least 50% higher than the average frequency for that nucleotide in the genome (≈20% for G and C, ≈30% for A and T). The most common nucleotide in each position is shaded.

Figure 5

Schematic of acetate and glucose utilization pathways in yeast. Glucose is metabolized by fermentation or respiration [via tricarboxylic acid (TCA) cycle]. Acetate is converted to acetyl-CoA and metabolized via the TCA cycle (respiration) and/or the glyoxylate cycle (which provides substrates for gluconeogenesis) (41, 42).