Yeast Carbon Catabolite Repression
01 Jun 1998-Microbiology and Molecular Biology Reviews (American Society for Microbiology)-Vol. 62, Iss: 2, pp 334-361
TL;DR: It is possible in certain cases to propose a partial model of the way in which the different elements involved in catabolite repression may be integrated, and preliminary evidence suggests that Snf1 is in a dephosphorylated state under these conditions.
Abstract: Glucose and related sugars repress the transcription of genes encoding enzymes required for the utilization of alternative carbon sources; some of these genes are also repressed by other sugars such as galactose, and the process is known as catabolite repression. The different sugars produce signals which modify the conformation of certain proteins that, in turn, directly or through a regulatory cascade affect the expression of the genes subject to catabolite repression. These genes are not all controlled by a single set of regulatory proteins, but there are different circuits of repression for different groups of genes. However, the protein kinase Snf1/Cat1 is shared by the various circuits and is therefore a central element in the regulatory process. Snf1 is not operative in the presence of glucose, and preliminary evidence suggests that Snf1 is in a dephosphorylated state under these conditions. However, the enzymes that phosphorylate and dephosphorylate Snf1 have not been identified, and it is not known how the presence of glucose may affect their activity. What has been established is that Snf1 remains active in mutants lacking either the proteins Grr1/Cat80 or Hxk2 or the Glc7 complex, which functions as a protein phosphatase. One of the main roles of Snf1 is to relieve repression by the Mig1 complex, but it is also required for the operation of transcription factors such as Adr1 and possibly other factors that are still unidentified. Although our knowledge of catabolite repression is still very incomplete, it is possible in certain cases to propose a partial model of the way in which the different elements involved in catabolite repression may be integrated.
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TL;DR: An integrated understanding of osmoadaptation requires not only knowledge of the function of many uncharacterized genes but also further insight into the time line of events, their interdependence, their dynamics, and their spatial organization as well as the importance of subtle effects.
Abstract: The ability to adapt to altered availability of free water is a fundamental property of living cells. The principles underlying osmoadaptation are well conserved. The yeast Saccharomyces cerevisiae is an excellent model system with which to study the molecular biology and physiology of osmoadaptation. Upon a shift to high osmolarity, yeast cells rapidly stimulate a mitogen-activated protein (MAP) kinase cascade, the high-osmolarity glycerol (HOG) pathway, which orchestrates part of the transcriptional response. The dynamic operation of the HOG pathway has been well studied, and similar osmosensing pathways exist in other eukaryotes. Protein kinase A, which seems to mediate a response to diverse stress conditions, is also involved in the transcriptional response program. Expression changes after a shift to high osmolarity aim at adjusting metabolism and the production of cellular protectants. Accumulation of the osmolyte glycerol, which is also controlled by altering transmembrane glycerol transport, is of central importance. Upon a shift from high to low osmolarity, yeast cells stimulate a different MAP kinase cascade, the cell integrity pathway. The transcriptional program upon hypo-osmotic shock seems to aim at adjusting cell surface properties. Rapid export of glycerol is an important event in adaptation to low osmolarity. Osmoadaptation, adjustment of cell surface properties, and the control of cell morphogenesis, growth, and proliferation are highly coordinated processes. The Skn7p response regulator may be involved in coordinating these events. An integrated understanding of osmoadaptation requires not only knowledge of the function of many uncharacterized genes but also further insight into the time line of events, their interdependence, their dynamics, and their spatial organization as well as the importance of subtle effects.
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Additional excerpts
...Our data suggest such as the lac and trp operons ( Barkley et al., 1975; that these activities may be mediated by positive FXR Lane, 1986)....
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TL;DR: The various hemicelluloses structures present in lignocellulose, the range of pre-treatment and hydrolysis options including the enzymatic ones, and the role of different microbial strains on process integration aiming to reach a meaningful consolidated bioprocessing are reviewed.
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Cites background from "Yeast Carbon Catabolite Repression"
...high glycolytic flux (Gancedo, 1998) and repression of respiratory pathway (Salusjärvi et al....
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24 Jul 1998
TL;DR: The algorthim is the first for this problem with provable guarantees for the reconstruction of surfaces from unorganized sample points in IR3, based on the three-dimensional Voronoi diagram.
Abstract: Author(s): Amenta, Nina; Bern, Marshall; Kamvysselis, Manolis | Abstract: We describe our experience with a new algorithm for the reconstruction of surfaces from unorganized sample points in IR3. The algorthim is the first for this problem with provable guarantees. Given a ''good sample'' from a smooth surface, the output is guaranteed to be topologically correct and convergent to the original surface as the sampling sensity increases. The definition of a good sample is itself interesting: the required sampling density varies locally, rigorously capturing the intuitive notion that featureless areas can be reconstructed from fewer samples. The output mesh interpolates, rather than approximates, the input points. Our algorithm is based on the three-dimensional Voronoi diagram. Given a good program for thsi fundamental subroutine, the algorithm is quite easy to implement.
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Cites background from "Yeast Carbon Catabolite Repression"
...[38] Gancedo JM: Yeast carbon catabolite repression....
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...Many of these genes encode aerobic respiration enzymes, which are required for the switch from fermentation to respiration [38] [39]....
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TL;DR: Data indicate that AMPK transmits a portion of the signal by which muscle contraction increases glucose uptake, but other AMPK-independent pathways also contribute to the response.
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References
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TL;DR: DNA microarrays containing virtually every gene of Saccharomyces cerevisiae were used to carry out a comprehensive investigation of the temporal program of gene expression accompanying the metabolic shift from fermentation to respiration, and the expression patterns of many previously uncharacterized genes provided clues to their possible functions.
Abstract: DNA microarrays containing virtually every gene of Saccharomyces cerevisiae were used to carry out a comprehensive investigation of the temporal program of gene expression accompanying the metabolic shift from fermentation to respiration. The expression profiles observed for genes with known metabolic functions pointed to features of the metabolic reprogramming that occur during the diauxic shift, and the expression patterns of many previously uncharacterized genes provided clues to their possible functions. The same DNA microarrays were also used to identify genes whose expression was affected by deletion of the transcriptional co-repressor TUP1 or overexpression of the transcriptional activator YAP1. These results demonstrate the feasibility and utility of this approach to genomewide exploration of gene expression patterns.
4,792 citations
TL;DR: A new cellular p300/CBP-associated factor (P/CAF) having intrinsic histone acetylase activity has been identified that competes with E1A, a new adenoviral oncoprotein that induces progression through the cell cycle by binding to the products of the p300 and retinoblastoma gene families.
Abstract: The adenoviral oncoprotein E1A induces progression through the cell cycle by binding to the products of the p300/CBP and retinoblastoma gene families. A new cellular p300/CBP-associated factor (P/CAF) having intrinsic histone acetylase activity has been identified that competes with E1A. Exogenous expression of P/CAF in HeLa cells inhibits cell-cycle progression and counteracts the mitogenic activity of E1A. E1A disturbs the normal cellular interaction between p300/CBP and its associated histone acetylase.
1,525 citations
TL;DR: The central hypothesis is that the AMP-activated protein kinase cascade appears to be an ancient system which evolved to protect cells against the effects of nutritional or environmental stress, and protects the cell by switching off ATP-consuming pathways and switching on alternative pathways for ATP generation.
Abstract: A single entity, the AMP-activated protein kinase (AMPK), phosphorylates and regulates in vivo hydroxymethylglutaryl-CoA reductase and acetyl-CoA carboxylase (key regulatory enzymes of sterol synthesis and fatty acid synthesis, respectively), and probably many additional targets. The kinase is activated by high AMP and low ATP via a complex mechanism, which involves allosteric regulation, promotion of phosphorylation by an upstream protein kinase (AMPK kinase), and inhibition of dephosphorylation. This protein-kinase cascade represents a sensitive system, which is activated by cellular stresses that deplete ATP, and thus acts like a cellular fuel gauge. Our central hypothesis is that, when it detects a 'low-fuel' situation, it protects the cell by switching off ATP-consuming pathways (e.g. fatty acid synthesis and sterol synthesis) and switching on alternative pathways for ATP generation (e.g. fatty acid oxidation). Native AMP-activated protein kinase is a heterotrimer consisting of a catalytic alpha subunit, and beta and gamma subunits, which are also essential for activity. All three subunits have homologues in budding yeast, which are components of the SNF1 protein-kinase complex. SNF1 is activated by glucose starvation (which in yeast leads to ATP depletion) and genetic studies have shown that it is involved in derepression of glucose-repressed genes. This raises the intriguing possibility that AMPK may regulate gene expression in mammals. AMPK/SNF1 homologues are found in higher plants, and this protein-kinase cascade appears to be an ancient system which evolved to protect cells against the effects of nutritional or environmental stress.
1,310 citations
TL;DR: A model is proposed to account for the synthesis and regulation of the two forms of inverts: the larger, regulated mRNA contains the initiation codon for the signal sequence required for synthesis of the secreted, glycosylated form of invertase; the smaller, constitutively transcribed mRNA begins within the coding region of the signal sequences, resulting in synthesis ofThe intracellular enzyme.
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TL;DR: This finding is consistent with the recent report that the AMP-activated protein kinase kinase can slowly phosphorylate and activate calmodulin-dependentprotein kinase I, at least in vitro.
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