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 ume6⌬ 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 carbon͞nitrogen metabolism and͞or 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.

Perturbation of the Activity of Replication Origin by Meiosis-specific Transcription

“…The transcription of MSH4 was induced at between one and two hours and reached the level of 10-fold of time 0 at three hours after the induction of meiosis, which is in good agreement with the previous data (24). The level of MSH4 transcripts at 3 h was maintained at the same level up to 5 h (data not shown), suggesting that MSH4 was transcribed actively during the premeiotic S-phase.…”

“…To determine the period of the premeiotic S-phase precisely, we assessed the progression of meiotic cell cycle by FACS and by microscopic observation of nuclear division. We used the SK1 strain as a wild type because of its efficient sporulation properties compared with other strains (24). We determined that 90% of cells entered premeiotic S-phase between 1-2 h and finished around 4 -5 h after induction, judging from the FACS profile and kinetics of meiotic divisions (Fig.…”

Ume6 transcription factor is part of a signaling cascade that regulates autophagy

“…1A), which was previously identified during a whole-genome microarray analysis (9)(10)(11). The URS1 consensus site consists of two invariant GGC repeats, which tend to be immediately preceded by a C and several T nucleotides and followed by a T and two A nucleotides, although some variability exists in these positions (9). We examined the promoter regions of other ATG genes and note that the gene encoding Atg23 also contains a potential URS1 site.…”

“…We examined the promoter regions of other ATG genes and note that the gene encoding Atg23 also contains a potential URS1 site. Ume6 is a zinc cluster protein that both represses and activates transcription of a diverse set of genes involved in meiosis and metabolism in response to nutritional cues such as glucose, nitrogen, and inositol (9,(12)(13)(14). If Ume6 regulates Atg8, then a ume6Δ strain should have altered Atg8 protein levels.…”

“…To identify candidate transcriptional regulators of ATG8, we analyzed its promoter region and identified an upstream regulatory sequence, URS1, which is a consensus binding site for the transcription factor Ume6 (Fig. 1A), which was previously identified during a whole-genome microarray analysis (9)(10)(11). The URS1 consensus site consists of two invariant GGC repeats, which tend to be immediately preceded by a C and several T nucleotides and followed by a T and two A nucleotides, although some variability exists in these positions (9).…”