Protein Kinase A, TOR, and Glucose Transport Control the Response to Nutrient Repletion in Saccharomyces cerevisiae

School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA.
Eukaryotic Cell (Impact Factor: 3.18). 03/2008; 7(2):358-67. DOI: 10.1128/EC.00334-07
Source: PubMed


Nutrient repletion leads to substantial restructuring of the transcriptome in Saccharomyces cerevisiae. The expression levels of approximately one-third of all S. cerevisiae genes are altered at least twofold when a nutrient-depleted culture is transferred to fresh medium. Several nutrient-sensing pathways are known to play a role in this process, but the relative contribution that each pathway makes to the total response has not been determined. To better understand this, we used a chemical-genetic approach to block the protein kinase A (PKA), TOR (target of rapamycin), and glucose transport pathways, alone and in combination. Of the three pathways, we found that loss of PKA produced the largest effect on the transcriptional response; however, many genes required both PKA and TOR for proper nutrient regulation. Those genes that did not require PKA or TOR for nutrient regulation were dependent on glucose transport for either nutrient induction or repression. Therefore, loss of these three pathways is sufficient to prevent virtually the entire transcriptional response to fresh medium. In the absence of fresh medium, activation of the cyclic AMP/PKA pathway does not induce cellular growth; nevertheless, PKA activation induced a substantial fraction of the PKA-dependent genes. In contrast, the absence of fresh medium strongly limited gene repression by PKA. These results account for the signals needed to generate the transcriptional responses to glucose, including induction of growth genes required for protein synthesis and repression of stress genes, as well as the classical glucose repression and hexose transporter responses.

Download full-text


Available from: Matthew Slattery,
  • Source
    • "Finally, we found that a ceased flux through the PP pathway is the last stage of the adaptation, occurring only 6 h after glucose depletion, which is accompanied by a change in NADPH source (Figure 5, 'III'). Moreover, we identify several reactions in the metabolic network (Figure 5, 'Regulatory site'), whose regulation most likely causes the observed changes in flux distribution (Figure 5, 'Fluxes') and the influence of metabolites levels Figure 5 Time-course reconstruction of the different events that lead to the adaptation based on the results presented in this report (regular text and solid arrows) and also supported by studies that were previously published (italics and dashed arrows) (Boy-Marcotte et al, 1996, 1998; DeRisi et al, 1997; Vincent and Carlson, 1998; Haurie et al, 2001; Haurie et al, 2004; Brauer et al, 2005; Radonjic et al, 2005; Slattery et al, 2008). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The diauxic shift in Saccharomyces cerevisiae is an ideal model to study how eukaryotic cells readjust their metabolism from glycolytic to gluconeogenic operation. In this work, we generated time-resolved physiological data, quantitative metabolome (69 intracellular metabolites) and proteome (72 enzymes) profiles. We found that the diauxic shift is accomplished by three key events that are temporally organized: (i) a reduction in the glycolytic flux and the production of storage compounds before glucose depletion, mediated by downregulation of phosphofructokinase and pyruvate kinase reactions; (ii) upon glucose exhaustion, the reversion of carbon flow through glycolysis and onset of the glyoxylate cycle operation triggered by an increased expression of the enzymes that catalyze the malate synthase and cytosolic citrate synthase reactions; and (iii) in the later stages of the adaptation, the shutting down of the pentose phosphate pathway with a change in NADPH regeneration. Moreover, we identified the transcription factors associated with the observed changes in protein abundances. Taken together, our results represent an important contribution toward a systems-level understanding of how this adaptation is realized.
    Molecular Systems Biology 04/2013; 9(1):651. DOI:10.1038/msb.2013.11 · 10.87 Impact Factor
  • Source
    • "Catabolite derepression, from a genetic point of view, results in transcription of numerous genes, by upstream activation sites (UAS) such as CCAAT box, R box, or CSRE element which are known to be involved in oxidative metabolic pathways [17] or PKA pathway [18, 19], and from a metabolic and functional point of view results in enhanced uptake of amino acids via TOR signal transduction [5]. Our results indicate a level of coordination between the genes activated during catabolite derepression via the UAS and via signal transduction through TOR, although the precise nature of this coordination remains an outstanding question. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Catabolite repression (CCR) regulates amino acid permeases in Saccharomyces cerevisiae via a TOR-kinase mediated mechanism. When glucose, the preferred fuel in S. cerevisiae, is substituted by galactose, amino acid uptake is increased. Here we have assessed the contribution and metabolic significance of this surfeit of amino acid in yeast undergoing catabolite derepression (CDR). L-[U-(14)C]leucine oxidation was increased 15 ± 1 fold in wild type (WT) strain grown in galactose compared to glucose. Under CDR, leucine oxidation was (i) proportional to uptake, as demonstrated by decreased uptake and oxidation of leucine in strains deleted of major leucine permeases and (ii) entirely dependent upon the TCA cycle, as cytochrome c1 (Cyt1) deleted strains could not grow in galactose. A regulator of amino acid carbon entry into the TCA cycle, branched chain ketoacid dehydrogenase, was also increased 29 ± 3 fold under CCR in WT strain. Protein expression of key TCA cycle enzymes, citrate synthase (Cs), and Cyt1 was increased during CDR. In summary, CDR upregulation of amino acid uptake is accompanied by increased utilization of amino acids for yeast growth. The mechanism for this is likely to be an increase in protein expression of key regulators of the TCA cycle.
    02/2013; 2013:461901. DOI:10.1155/2013/461901
  • Source
    • "Furthermore, cAMP was able to produce similar transcriptional responses to those produced by N or P repletion. We have previously observed very similar results with G repletion (Slattery et al. 2008). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Saccharomyces cerevisiae are able to control growth in response to changes in nutrient availability. The limitation for single macronutrients, including nitrogen (N) and phosphate (P), produces stable arrest in G1/G0. Restoration of the limiting nutrient quickly restores growth. It has been shown that glucose (G) depletion/repletion very rapidly alters the levels of more than 2000 transcripts by at least 2-fold, a large portion of which are involved with either protein production in growth or stress responses in starvation. Although the signals generated by G, N, and P are thought to be quite distinct, we tested the hypothesis that depletion and repletion of any of these three nutrients would affect a common core set of genes as part of a generalized response to conditions that promote growth and quiescence. We found that the response to depletion of G, N, or P produced similar quiescent states with largely similar transcriptomes. As we predicted, repletion of each of the nutrients G, N, or P induced a large (501) common core set of genes and repressed a large (616) common gene set. Each nutrient also produced nutrient-specific transcript changes. The transcriptional responses to each of the three nutrients depended on cAMP and, to a lesser extent, the TOR pathway. All three nutrients stimulated cAMP production within minutes of repletion, and artificially increasing cAMP levels was sufficient to replicate much of the core transcriptional response. The recently identified transceptors Gap1, Mep1, Mep2, and Mep3, as well as Pho84, all played some role in the core transcriptional responses to N or P. As expected, we found some evidence of cross talk between nutrient signals, yet each nutrient sends distinct signals.
    G3-Genes Genomes Genetics 09/2012; 2(9):1003-17. DOI:10.1534/g3.112.002808 · 3.20 Impact Factor
Show more