Multiple Pathways Are Co-regulated by the Protein Kinase Snf1 and the Transcription Factors Adr1 and Cat8

Abstract

ADR1 and CAT8 encode carbon source-responsive transcriptional regulators that cooperatively control expression of genes involved in ethanol utilization. These transcription factors are active only after the diauxic transition, when glucose is depleted and energy-generating metabolism has shifted to the aerobic oxidation of non-fermentable carbon sources. The Snf1 protein kinase complex is required for activation of their downstream target genes described previously. Using DNA microarrays, we determined the extent to which these three factors collaborate in regulating the expression of the yeast genome after glucose depletion. The expression of 108 genes is significantly decreased in the absence of ADR1. The importance of ADR1 during the diauxic transition is illustrated by the observation that expression of almost one-half of the 40 most highly glucose-repressed genes is ADR1-dependent. ADR1-dependent genes fall into a variety of functional classes with carbon metabolism containing the largest number of members. Most of the genes in this class are involved in the oxidation of different non-fermentable carbon sources. These microarray data show that ADR1 coordinates the biochemical pathways that generate acetylCoA and NADH from non-fermentable substrates. Only a small number of ADR1-dependent genes are also CAT8-dependent. However, nearly one-half of the ADR1-dependent genes are also dependent on the Snf1 protein kinase for derepression. Many more genes are SNF1-dependent than are either ADR1-or CAT8-dependent suggesting that SNF1 plays a broader role in gene expression than either ADR1 or CAT8. The largest class of SNF1-dependent genes encodes regulatory proteins that could extend SNF1 dependence to additional pathways.During the diauxic shift, when yeast cells deplete the glucose in the medium, the flow of metabolites changes dramatically to adapt to the use of alternative energy and carbon sources, primarily ethanol produced during fermentation. The changes in gene expression that are required for this metabolic reorganization were dramatically revealed by DNA microarray analysis (1). The expression of more than one-quarter of the yeast genome is altered when glucose is exhausted. These alterations allow the cell to utilize carbon sources other than glucose to channel metabolites into the tricarboxylic acid and glyoxylate cycles to generate energy and synthesize intermediates for gluconeogenesis. In addition, these changes allow the cell to alter its growth rate and prepare for growth arrest and stationary phase.Numerous transcription factors and regulatory proteins are responsible for the altered transcriptional program that accompanies the depletion of glucose. Two transcription factors that play important roles during the diauxic transition are Adr1 1 and Cat8.

Ubp8 and SAGA Regulate Snf1 AMP Kinase Activity

“…This overlap in function at these genes supports the idea that Ubp8 modulates the activity of Snf1 to fine-tune the regulation of Snf1 target genes ( Fig. 5A and Table 2) (16,40,45). To more directly determine whether Snf1 activity is affected by Ubp8 loss, we examined the phosphorylation status of a Snf1 target protein.…”

“…If so, then loss of Ubp8 might cause changes in gene expression similar to those caused by loss of Snf1. Therefore, we examined previously published microarray data and found significant overlaps between changes in gene expression reported for snf1⌬ and ubp8⌬ strains (16,45). However, it is difficult to distinguish which changes are direct or indirect, as the SAGA complex and Snf1 each regulate many genes (Table 2).…”

Changes in Transcription and Metabolism During the Early Stage of Replicative Cellular Senescence in Budding Yeast

“…High expression of stationary phaseinduced genes after 11 generations indicated that transcription factors induce gene expression during stationary phase and regulate the transcription of senescence-induced genes. For example, Msn2p/Msn4p and Gis1p in the Rim15p protein kinase pathway and Adr1p, Cat8p, and Mig1p in the Snf1p protein kinase pathway are thought to be transcription factors that regulate stationary phase-induced genes (33,34). Transcription of the MSN2, MSN4, GIS1, and CAT8 genes was not regulated during the early stage of senescence, but the ADR1 activator gene was up-regulated 4-fold, and MIG1 repressor gene was down-regulated 2-fold at the 11th generation relative to the 1st generation.…”

β-Subunits of the SnRK1 Complexes Share a Common Ancestral Function Together with Expression and Function Specificities; Physical Interaction with Nitrate Reductase Specifically Occurs via AKINβ1-Subunit

“…This ancestral function could concern the control of carbohydrate and energy metabolism. Indeed, in response to Glc or energy deprivation in yeast, SNF1 is necessary for the transition from fermentative to oxidative metabolism (Hardie et al, 1998;Young et al, 2003) and AMPK in mammals plays a central role in the energy balance at the whole body level by synchronizing several metabolic pathways Carling, 2004). In plants, a recent work reports an inhibition of SnRK1 by sugars and strongly supports the idea that SnRK1 is a central regulator of plant metabolism and energy balance in response to sugar level (Baena-González et al, 2007).…”

“…In yeast, SNF1 (for Suc nonfermenting 1) is as a key player in the shift from fermentative to oxidative metabolism in response to Glc deprivation (diauxic shift; Hardie et al, 1998). Indeed, a quarter of the genome presents a SNF1-dependent change in expression during this shift (Young et al, 2003). In mammals, AMPK, the SNF1 homolog, has been involved in sensing the cellular and whole-body energy levels.…”