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Persson S, Welkenhuysen N, Shashkova S, Wiqvist S, Reith P, Schmidt GW, Picchini U, Cvijovic M. Scalable and flexible inference framework for stochastic dynamic single-cell models. PLoS Comput Biol 2022; 18:e1010082. [PMID: 35588132 PMCID: PMC9159578 DOI: 10.1371/journal.pcbi.1010082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 06/01/2022] [Accepted: 04/05/2022] [Indexed: 01/22/2023] Open
Abstract
Understanding the inherited nature of how biological processes dynamically change over time and exhibit intra- and inter-individual variability, due to the different responses to environmental stimuli and when interacting with other processes, has been a major focus of systems biology. The rise of single-cell fluorescent microscopy has enabled the study of those phenomena. The analysis of single-cell data with mechanistic models offers an invaluable tool to describe dynamic cellular processes and to rationalise cell-to-cell variability within the population. However, extracting mechanistic information from single-cell data has proven difficult. This requires statistical methods to infer unknown model parameters from dynamic, multi-individual data accounting for heterogeneity caused by both intrinsic (e.g. variations in chemical reactions) and extrinsic (e.g. variability in protein concentrations) noise. Although several inference methods exist, the availability of efficient, general and accessible methods that facilitate modelling of single-cell data, remains lacking. Here we present a scalable and flexible framework for Bayesian inference in state-space mixed-effects single-cell models with stochastic dynamic. Our approach infers model parameters when intrinsic noise is modelled by either exact or approximate stochastic simulators, and when extrinsic noise is modelled by either time-varying, or time-constant parameters that vary between cells. We demonstrate the relevance of our approach by studying how cell-to-cell variation in carbon source utilisation affects heterogeneity in the budding yeast Saccharomyces cerevisiae SNF1 nutrient sensing pathway. We identify hexokinase activity as a source of extrinsic noise and deduce that sugar availability dictates cell-to-cell variability.
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Affiliation(s)
- Sebastian Persson
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Niek Welkenhuysen
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Sviatlana Shashkova
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Physics, University of Gothenburg, Gothenburg, Sweden
| | - Samuel Wiqvist
- Centre for Mathematical Sciences, Lund University, Lund, Sweden
| | - Patrick Reith
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Gregor W. Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Umberto Picchini
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
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2
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Persson S, Shashkova S, Österberg L, Cvijovic M. Modelling of glucose repression signalling in yeast Saccharomyces cerevisiae. FEMS Yeast Res 2022; 22:foac012. [PMID: 35238938 PMCID: PMC8916112 DOI: 10.1093/femsyr/foac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/11/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Saccharomyces cerevisiae has a sophisticated signalling system that plays a crucial role in cellular adaptation to changing environments. The SNF1 pathway regulates energy homeostasis upon glucose derepression; hence, it plays an important role in various processes, such as metabolism, cell cycle and autophagy. To unravel its behaviour, SNF1 signalling has been extensively studied. However, the pathway components are strongly interconnected and inconstant; therefore, elucidating its dynamic behaviour based on experimental data only is challenging. To tackle this complexity, systems biology approaches have been successfully employed. This review summarizes the progress, advantages and disadvantages of the available mathematical modelling frameworks covering Boolean, dynamic kinetic, single-cell models, which have been used to study processes and phenomena ranging from crosstalks to sources of cell-to-cell variability in the context of SNF1 signalling. Based on the lessons from existing models, we further discuss how to develop a consensus dynamic mechanistic model of the entire SNF1 pathway that can provide novel insights into the dynamics of nutrient signalling.
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Affiliation(s)
- Sebastian Persson
- Department of Mathematical Sciences, Chalmers University of Technology, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
| | - Sviatlana Shashkova
- Department of Mathematical Sciences, Chalmers University of Technology, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
| | - Linnea Österberg
- Department of Mathematical Sciences, Chalmers University of Technology, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, Chalmers University of Technology, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
- Department of Mathematical Sciences, University of Gothenburg, Chalmers tvärgata 3, 412 96 Gothnburg, Sweden
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3
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Shashkova S, Nyström T, Leake MC, Wollman AJM. Correlative single-molecule fluorescence barcoding of gene regulation in Saccharomyces cerevisiae. Methods 2020; 193:62-67. [PMID: 33086048 PMCID: PMC8343463 DOI: 10.1016/j.ymeth.2020.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/07/2020] [Accepted: 10/15/2020] [Indexed: 01/14/2023] Open
Abstract
Most cells adapt to their environment by switching combinations of genes on and off through a complex interplay of transcription factor proteins (TFs). The mechanisms by which TFs respond to signals, move into the nucleus and find specific binding sites in target genes is still largely unknown. Single-molecule fluorescence microscopes, which can image single TFs in live cells, have begun to elucidate the problem. Here, we show that different environmental signals, in this case carbon sources, yield a unique single-molecule fluorescence pattern of foci of a key metabolic regulating transcription factor, Mig1, in the nucleus of the budding yeast, Saccharomyces cerevisiae. This pattern serves as a 'barcode' of the gene regulatory state of the cells which can be correlated with cell growth characteristics and other biological function.
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Affiliation(s)
- Sviatlana Shashkova
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden.
| | - Thomas Nyström
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden.
| | - Mark C Leake
- Department of Physics, University of York, YO10 5DD York, United Kingdom.
| | - Adam J M Wollman
- Newcastle University Biosciences Institute, Newcastle NE2 4HH, United Kingdom.
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4
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Persson S, Welkenhuysen N, Shashkova S, Cvijovic M. Fine-Tuning of Energy Levels Regulates SUC2 via a SNF1-Dependent Feedback Loop. Front Physiol 2020; 11:954. [PMID: 32922308 PMCID: PMC7456839 DOI: 10.3389/fphys.2020.00954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/15/2020] [Indexed: 11/22/2022] Open
Abstract
Nutrient sensing pathways are playing an important role in cellular response to different energy levels. In budding yeast, Saccharomyces cerevisiae, the sucrose non-fermenting protein kinase complex SNF1 is a master regulator of energy homeostasis. It is affected by multiple inputs, among which energy levels is the most prominent. Cells which are exposed to a switch in carbon source availability display a change in the gene expression machinery. It has been shown that the magnitude of the change varies from cell to cell. In a glucose rich environment Snf1/Mig1 pathway represses the expression of its downstream target, such as SUC2. However, upon glucose depletion SNF1 is activated which leads to an increase in SUC2 expression. Our single cell experiments indicate that upon starvation, gene expression pattern of SUC2 shows rapid increase followed by a decrease to initial state with high cell-to-cell variability. The mechanism behind this behavior is currently unknown. In this work we study the long-term behavior of the Snf1/Mig1 pathway upon glucose starvation with a microfluidics and non-linear mixed effect modeling approach. We show a negative feedback mechanism, involving Snf1 and Reg1, which reduces SUC2 expression after the initial strong activation. Snf1 kinase activity plays a key role in this feedback mechanism. Our systems biology approach proposes a negative feedback mechanism that works through the SNF1 complex and is controlled by energy levels. We further show that Reg1 likely is involved in the negative feedback mechanism.
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Affiliation(s)
- Sebastian Persson
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Niek Welkenhuysen
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Sviatlana Shashkova
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
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5
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Nishimura A, Nasuno R, Yoshikawa Y, Jung M, Ida T, Matsunaga T, Morita M, Takagi H, Motohashi H, Akaike T. Mitochondrial cysteinyl-tRNA synthetase is expressed via alternative transcriptional initiation regulated by energy metabolism in yeast cells. J Biol Chem 2019; 294:13781-13788. [PMID: 31350340 DOI: 10.1074/jbc.ra119.009203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/23/2019] [Indexed: 11/06/2022] Open
Abstract
Eukaryotes typically utilize two distinct aminoacyl-tRNA synthetase isoforms, one for cytosolic and one for mitochondrial protein synthesis. However, the genome of budding yeast (Saccharomyces cerevisiae) contains only one cysteinyl-tRNA synthetase gene (YNL247W, also known as CRS1). In this study, we report that CRS1 encodes both cytosolic and mitochondrial isoforms. The 5' complementary DNA end method and GFP reporter gene analyses indicated that yeast CRS1 expression yields two classes of mRNAs through alternative transcription starts: a long mRNA containing a mitochondrial targeting sequence and a short mRNA lacking this targeting sequence. We found that the mitochondrial Crs1 is the product of translation from the first initiation AUG codon on the long mRNA, whereas the cytosolic Crs1 is produced from the second in-frame AUG codon on the short mRNA. Genetic analysis and a ChIP assay revealed that the transcription factor heme activator protein (Hap) complex, which is involved in mitochondrial biogenesis, determines the transcription start sites of the CRS1 gene. We also noted that Hap complex-dependent initiation is regulated according to the needs of mitochondrial energy production. The results of our study indicate energy-dependent initiation of alternative transcription of CRS1 that results in production of two Crs1 isoforms, a finding that suggests Crs1's potential involvement in mitochondrial energy metabolism in yeast.
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Affiliation(s)
- Akira Nishimura
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Ryo Nasuno
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Yuki Yoshikawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Minkyung Jung
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Tomoaki Ida
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Tetsuro Matsunaga
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Masanobu Morita
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
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6
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Shashkova S, Wollman AJM, Leake MC, Hohmann S. The yeast Mig1 transcriptional repressor is dephosphorylated by glucose-dependent and -independent mechanisms. FEMS Microbiol Lett 2018; 364:3884263. [PMID: 28854669 DOI: 10.1093/femsle/fnx133] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 06/21/2017] [Indexed: 12/28/2022] Open
Abstract
A yeast Saccharomyces cerevisiae Snf1 kinase, an analog of mammalian AMPK, regulates glucose derepression of genes required for utilization of alternative carbon sources through the transcriptional repressor Mig1. It has been suggested that the Glc7-Reg1 phosphatase dephosphorylates Mig1. Here we report that Mig1 is dephosphorylated by Glc7-Reg1 in an apparently glucose-dependent mechanism but also by a mechanism independent of glucose and Glc7-Reg1. In addition to serine/threonine phosphatases another process including tyrosine phosphorylation seems crucial for Mig1 regulation. Taken together, Mig1 dephosphorylation appears to be controlled in a complex manner, in line with the importance for rapid and sensitive regulation upon altered glucose concentrations in the growth medium.
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Affiliation(s)
- Sviatlana Shashkova
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Göteborg, Sweden.,Biological Physical Sciences Institute, University of York, York YO10 5DD, UK
| | - Adam J M Wollman
- Biological Physical Sciences Institute, University of York, York YO10 5DD, UK
| | - Mark C Leake
- Biological Physical Sciences Institute, University of York, York YO10 5DD, UK
| | - Stefan Hohmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Göteborg, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Göteborg, Sweden
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7
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Sugar and Glycerol Transport in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:125-168. [PMID: 26721273 DOI: 10.1007/978-3-319-25304-6_6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In Saccharomyces cerevisiae the process of transport of sugar substrates into the cell comprises a complex network of transporters and interacting regulatory mechanisms. Members of the large family of hexose (HXT) transporters display uptake efficiencies consistent with their environmental expression and play physiological roles in addition to feeding the glycolytic pathway. Multiple glucose-inducing and glucose-independent mechanisms serve to regulate expression of the sugar transporters in yeast assuring that expression levels and transporter activity are coordinated with cellular metabolism and energy needs. The expression of sugar transport activity is modulated by other nutritional and environmental factors that may override glucose-generated signals. Transporter expression and activity is regulated transcriptionally, post-transcriptionally and post-translationally. Recent studies have expanded upon this suite of regulatory mechanisms to include transcriptional expression fine tuning mediated by antisense RNA and prion-based regulation of transcription. Much remains to be learned about cell biology from the continued analysis of this dynamic process of substrate acquisition.
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8
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Lubitz T, Welkenhuysen N, Shashkova S, Bendrioua L, Hohmann S, Klipp E, Krantz M. Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review. NPJ Syst Biol Appl 2015; 1:15007. [PMID: 28725459 PMCID: PMC5516868 DOI: 10.1038/npjsba.2015.7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 06/19/2015] [Accepted: 07/14/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND/OBJECTIVES The SNF1/AMPK protein kinase has a central role in energy homeostasis in eukaryotic cells. It is activated by energy depletion and stimulates processes leading to the production of ATP while it downregulates ATP-consuming processes. The yeast SNF1 complex is best known for its role in glucose derepression. METHODS We performed a network reconstruction of the Snf1 pathway based on a comprehensive literature review. The network was formalised in the rxncon language, and we used the rxncon toolbox for model validation and gap filling. RESULTS We present a machine-readable network definition that summarises the mechanistic knowledge of the Snf1 pathway. Furthermore, we used the known input/output relationships in the network to identify and fill gaps in the information transfer through the pathway, to produce a functional network model. Finally, we convert the functional network model into a rule-based model as a proof-of-principle. CONCLUSIONS The workflow presented here enables large scale reconstruction, validation and gap filling of signal transduction networks. It is analogous to but distinct from that established for metabolic networks. We demonstrate the workflow capabilities, and the direct link between the reconstruction and dynamic modelling, with the Snf1 network. This network is a distillation of the knowledge from all previous publications on the Snf1/AMPK pathway. The network is a knowledge resource for modellers and experimentalists alike, and a template for similar efforts in higher eukaryotes. Finally, we envisage the workflow as an instrumental tool for reconstruction of large signalling networks across Eukaryota.
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Affiliation(s)
- Timo Lubitz
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Niek Welkenhuysen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Sviatlana Shashkova
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Loubna Bendrioua
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Stefan Hohmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marcus Krantz
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
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9
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Shashkova S, Welkenhuysen N, Hohmann S. Molecular communication: crosstalk between the Snf1 and other signaling pathways. FEMS Yeast Res 2015; 15:fov026. [DOI: 10.1093/femsyr/fov026] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2015] [Indexed: 02/02/2023] Open
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10
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Bendrioua L, Smedh M, Almquist J, Cvijovic M, Jirstrand M, Goksör M, Adiels CB, Hohmann S. Yeast AMP-activated protein kinase monitors glucose concentration changes and absolute glucose levels. J Biol Chem 2014; 289:12863-75. [PMID: 24627493 DOI: 10.1074/jbc.m114.547976] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Analysis of the time-dependent behavior of a signaling system can provide insight into its dynamic properties. We employed the nucleocytoplasmic shuttling of the transcriptional repressor Mig1 as readout to characterize Snf1-Mig1 dynamics in single yeast cells. Mig1 binds to promoters of target genes and mediates glucose repression. Mig1 is predominantly located in the nucleus when glucose is abundant. Upon glucose depletion, Mig1 is phosphorylated by the yeast AMP-activated kinase Snf1 and exported into the cytoplasm. We used a three-channel microfluidic device to establish a high degree of control over the glucose concentration exposed to cells. Following regimes of glucose up- and downshifts, we observed a very rapid response reaching a new steady state within less than 1 min, different glucose threshold concentrations depending on glucose up- or downshifts, a graded profile with increased cell-to-cell variation at threshold glucose concentrations, and biphasic behavior with a transient translocation of Mig1 upon the shift from high to intermediate glucose concentrations. Fluorescence loss in photobleaching and fluorescence recovery after photobleaching data demonstrate that Mig1 shuttles constantly between the nucleus and cytoplasm, although with different rates, depending on the presence of glucose. Taken together, our data suggest that the Snf1-Mig1 system has the ability to monitor glucose concentration changes as well as absolute glucose levels. The sensitivity over a wide range of glucose levels and different glucose concentration-dependent response profiles are likely determined by the close integration of signaling with the metabolism and may provide for a highly flexible and fast adaptation to an altered nutritional status.
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Affiliation(s)
- Loubna Bendrioua
- From the Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Göteborg, Sweden
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11
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Ye C, Lou W, Li Y, Chatzispyrou IA, Hüttemann M, Lee I, Houtkooper RH, Vaz FM, Chen S, Greenberg ML. Deletion of the cardiolipin-specific phospholipase Cld1 rescues growth and life span defects in the tafazzin mutant: implications for Barth syndrome. J Biol Chem 2013; 289:3114-25. [PMID: 24318983 DOI: 10.1074/jbc.m113.529487] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cardiolipin (CL) that is synthesized de novo is deacylated to monolysocardiolipin (MLCL), which is reacylated by tafazzin. Remodeled CL contains mostly unsaturated fatty acids. In eukaryotes, loss of tafazzin leads to growth and respiration defects, and in humans, this results in the life-threatening disorder Barth syndrome. Tafazzin deficiency causes a decrease in the CL/MLCL ratio and decreased unsaturated CL species. Which of these biochemical outcomes contributes to the physiological defects is not known. Yeast cells have a single CL-specific phospholipase, Cld1, that can be exploited to distinguish between these outcomes. The cld1Δ mutant has decreased unsaturated CL, but the CL/MLCL ratio is similar to that of wild type cells. We show that cld1Δ rescues growth, life span, and respiratory defects of the taz1Δ mutant. This suggests that defective growth and respiration in tafazzin-deficient cells are caused by the decreased CL/MLCL ratio and not by a deficiency in unsaturated CL. CLD1 expression is increased during respiratory growth and regulated by the heme activator protein transcriptional activation complex. Overexpression of CLD1 leads to decreased mitochondrial respiration and growth and instability of mitochondrial DNA. However, ATP concentrations are maintained by increasing glycolysis. We conclude that transcriptional regulation of Cld1-mediated deacylation of CL influences energy metabolism by modulating the relative contribution of glycolysis and respiration.
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Affiliation(s)
- Cunqi Ye
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
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12
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Sun J, Glass NL. Identification of the CRE-1 cellulolytic regulon in Neurospora crassa. PLoS One 2011; 6:e25654. [PMID: 21980519 PMCID: PMC3183063 DOI: 10.1371/journal.pone.0025654] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/09/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In filamentous ascomycete fungi, the utilization of alternate carbon sources is influenced by the zinc finger transcription factor CreA/CRE-1, which encodes a carbon catabolite repressor protein homologous to Mig1 from Saccharomyces cerevisiae. In Neurospora crassa, deletion of cre-1 results in increased secretion of amylase and β-galactosidase. METHODOLOGY/PRINCIPAL FINDINGS Here we show that a strain carrying a deletion of cre-1 has increased cellulolytic activity and increased expression of cellulolytic genes during growth on crystalline cellulose (Avicel). Constitutive expression of cre-1 complements the phenotype of a N. crassa Δcre-1 strain grown on Avicel, and also results in stronger repression of cellulolytic protein secretion and enzyme activity. We determined the CRE-1 regulon by investigating the secretome and transcriptome of a Δcre-1 strain as compared to wild type when grown on Avicel versus minimal medium. Chromatin immunoprecipitation-PCR of putative target genes showed that CRE-1 binds to only some adjacent 5'-SYGGRG-3' motifs, consistent with previous findings in other fungi, and suggests that unidentified additional regulatory factors affect CRE-1 binding to promoter regions. Characterization of 30 mutants containing deletions in genes whose expression level increased in a Δcre-1 strain under cellulolytic conditions identified novel genes that affect cellulase activity and protein secretion. CONCLUSIONS/SIGNIFICANCE Our data provide comprehensive information on the CRE-1 regulon in N. crassa and contribute to deciphering the global role of carbon catabolite repression in filamentous ascomycete fungi during plant cell wall deconstruction.
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Affiliation(s)
- Jianping Sun
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- * E-mail:
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13
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Lavoie M, Ge D, Abou Elela S. Regulation of conditional gene expression by coupled transcription repression and RNA degradation. Nucleic Acids Res 2011; 40:871-83. [PMID: 21933814 PMCID: PMC3258148 DOI: 10.1093/nar/gkr759] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Gene expression is determined by a combination of transcriptional and post-transcriptional regulatory events that were thought to occur independently. This report demonstrates that the genes associated with the Snf3p–Rgt2p glucose-sensing pathway are regulated by interconnected transcription repression and RNA degradation. Deletion of the dsRNA-specific ribonuclease III Rnt1p increased the expression of Snf3p–Rgt2p-associated transcription factors in vivo and the recombinant enzyme degraded their messenger RNA in vitro. Surprisingly, Rnt1ps effect on gene expression in vivo was both RNA and promoter dependent, thus linking RNA degradation to transcription. Strikingly, deletion of RNT1-induced promoter-specific transcription of the glucose sensing genes even in the absence of RNA cleavage signals. Together, the results presented here support a model in which co-transcriptional RNA degradation increases the efficiency of gene repression, thereby allowing an effective cellular response to the continuous changes in nutrient concentrations.
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Affiliation(s)
- Mathieu Lavoie
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada, J1H 5N4
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14
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Role of chromatin states in transcriptional memory. Biochim Biophys Acta Gen Subj 2009; 1790:445-55. [PMID: 19236904 DOI: 10.1016/j.bbagen.2009.02.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/10/2009] [Accepted: 02/11/2009] [Indexed: 12/16/2022]
Abstract
Establishment of cellular memory and its faithful propagation is critical for successful development of multicellular organisms. As pluripotent cells differentiate, choices in cell fate are inherited and maintained by their progeny throughout the lifetime of the organism. A major factor in this process is the epigenetic inheritance of specific transcriptional states or transcriptional memory. In this review, we discuss chromatin transitions and mechanisms by which they are inherited by subsequent generations. We also discuss illuminating cases of cellular memory in budding yeast and evaluate whether transcriptional memory in yeast is nuclear or cytoplasmically inherited.
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15
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Gertz J, Cohen BA. Environment-specific combinatorial cis-regulation in synthetic promoters. Mol Syst Biol 2009; 5:244. [PMID: 19225457 PMCID: PMC2657533 DOI: 10.1038/msb.2009.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 01/05/2009] [Indexed: 01/27/2023] Open
Abstract
When a cell's environment changes, a large transcriptional response often takes place. The exquisite sensitivity and specificity of these responses are controlled in large part by the combinations of cis-regulatory elements that reside in gene promoters and adjacent control regions. Here, we present a study aimed at accurately modeling the relationship between combinations of cis-regulatory elements and the expression levels they drive in different environments. We constructed four libraries of synthetic promoters in yeast, consisting of combinations of transcription factor binding sites and assayed their expression in four different environments. Thermodynamic models relating promoter sequences to their corresponding four expression levels explained at least 56% of the variation in expression in each library through the different conditions. Analyses of these models suggested that a large fraction of regulated gene expression is explained by changes in the effective concentration of sequence-specific transcription factors, and we show that in most cases, the corresponding transcription factors are expressed in a pattern that is predicted by the thermodynamic models. Our analysis uncovered two binding sites that switch from activators to repressors in different environmental conditions. In both the cases, the switch was not the result of a single transcription factor changing regulatory modes, but most likely due to competition between multiple factors binding to the same site. Our analysis suggests that this mode of regulation allows for large and steep changes in expression in response to changing transcription factor concentrations. Our results demonstrate that many complex changes in gene expression are accurately explained by simple changes in the effective concentrations of transcription factors.
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Affiliation(s)
- Jason Gertz
- Center for Genome Sciences, Department of Genetics, Washington University in St Louis School of Medicine, St Louis, MO 63108, USA
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16
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Lim MK, Tang V, Le Saux A, Schüller J, Bongards C, Lehming N. Gal11p dosage-compensates transcriptional activator deletions via Taf14p. J Mol Biol 2007; 374:9-23. [PMID: 17919657 DOI: 10.1016/j.jmb.2007.09.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 08/04/2007] [Accepted: 09/04/2007] [Indexed: 10/22/2022]
Abstract
Transcriptional activators work by recruiting transcription factors that are required for the process of transcription to their target genes. We have used the Split-Ubiquitin system to identify eight transcription factors that interacted with both the transcriptional activators Gal4p and Gcn4p in living cells. The over-expression of one of the activator-interacting proteins, Gal11p, partially suppressed GAL4 and GCN4 deletions. We have isolated two point mutants in Gal11p, F848L and F869S that were defective for the dosage compensation. We have identified 35 transcription factors that interacted with Gal11p in living cells, and the only protein-protein interaction affected by the Gal11p mutations was the one between Gal11p and Taf14p. We have further shown that the suppression of a GAL4 deletion by high levels of Gal11p required Taf14p, and that over-expression of Gal11p recruited Taf14p to the GAL1 promoter together with Tbp1p, Swi2p and Srb7p. Gal11p interacted with Mig1p, indicating that Mig1/2p could have recruited Gal11p to the GAL1 promoter in the absence of Gal4p. Our results suggest that transcriptional activators work by raising the local concentration of the limiting factor Gal11p, and that Gal11p works by recruiting Mediator and Taf14p-containing transcription factors like TFIID and SWI/SNF and by competing general repressors like Ssn6p-Tup1p off the target promoters.
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Affiliation(s)
- Mei Kee Lim
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
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17
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Tanaka F, Ando A, Nakamura T, Takagi H, Shima J. Functional genomic analysis of commercial baker's yeast during initial stages of model dough-fermentation. Food Microbiol 2006; 23:717-28. [PMID: 16943074 DOI: 10.1016/j.fm.2006.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Revised: 02/09/2006] [Accepted: 02/09/2006] [Indexed: 12/21/2022]
Abstract
Gene expression profiles of baker's yeast during initial dough-fermentation were investigated using liquid fermentation (LF) media to obtain insights at the molecular level into rapid adaptation mechanisms of baker's yeast. Results showed that onset of fermentation caused drastic changes in gene expression profiles within 15 min. Genes involved in the tricarboxylic acid (TCA) cycle were down-regulated and genes involved in glycolysis were up-regulated, indicating a metabolic shift from respiration to fermentation. Genes involved in ethanol production (PDC genes and ADH1), in glycerol synthesis (GPD1 and HOR2), and in low-affinity hexose transporters (HXT1 and HXT3) were up-regulated at the beginning of model dough-fermentation. Among genes up-regulated at 15 min, several genes classified as transcription were down-regulated within 30 min. These down-regulated genes are involved in messenger RNA splicing and ribosomal protein biogenesis and in transcriptional regulator (SRB8, MIG1). In contrast, genes involved in amino acid metabolism and in vitamin metabolism, such as arginine biosynthesis, riboflavin biosynthesis, and thiamin biosynthesis, were subsequently up-regulated after 30 min. Interestingly, the genes involved in the unfolded protein response (UPR) pathway were also subsequently up-regulated. Our study presents the first overall description of the transcriptional response of baker's yeast during dough-fermentation, and will thus help clarify genomic responses to various stresses during commercial fermentation processes.
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Affiliation(s)
- Fumiko Tanaka
- National Food Research Institute, Tsukuba, Ibaraki, Japan
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18
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Abstract
Eukaryotic cells possess an exquisitely interwoven and fine-tuned series of signal transduction mechanisms with which to sense and respond to the ubiquitous fermentable carbon source glucose. The budding yeast Saccharomyces cerevisiae has proven to be a fertile model system with which to identify glucose signaling factors, determine the relevant functional and physical interrelationships, and characterize the corresponding metabolic, transcriptomic, and proteomic readouts. The early events in glucose signaling appear to require both extracellular sensing by transmembrane proteins and intracellular sensing by G proteins. Intermediate steps involve cAMP-dependent stimulation of protein kinase A (PKA) as well as one or more redundant PKA-independent pathways. The final steps are mediated by a relatively small collection of transcriptional regulators that collaborate closely to maximize the cellular rates of energy generation and growth. Understanding the nuclear events in this process may necessitate the further elaboration of a new model for eukaryotic gene regulation, called "reverse recruitment." An essential feature of this idea is that fine-structure mapping of nuclear architecture will be required to understand the reception of regulatory signals that emanate from the plasma membrane and cytoplasm. Completion of this task should result in a much improved understanding of eukaryotic growth, differentiation, and carcinogenesis.
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Affiliation(s)
- George M Santangelo
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406-5018, USA.
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19
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Liu Y, Xu X, Singh-Rodriguez S, Zhao Y, Kuo MH. Histone H3 Ser10 phosphorylation-independent function of Snf1 and Reg1 proteins rescues a gcn5- mutant in HIS3 expression. Mol Cell Biol 2005; 25:10566-79. [PMID: 16287868 PMCID: PMC1291248 DOI: 10.1128/mcb.25.23.10566-10579.2005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gcn5 protein is a prototypical histone acetyltransferase that controls transcription of multiple yeast genes. To identify molecular functions that act downstream of or in parallel with Gcn5 protein, we screened for suppressors that rescue the transcriptional defects of HIS3 caused by a catalytically inactive mutant Gcn5, the E173H mutant. One bypass of Gcn5 requirement gene (BGR) suppressor was mapped to the REG1 locus that encodes a semidominant mutant truncated after amino acid 740. Reg1(1-740) protein does not rescue the complete knockout of GCN5, nor does it suppress other gcn5- defects, including the inability to utilize nonglucose carbon sources. Reg1(1-740) enhances HIS3 transcription while HIS3 promoter remains hypoacetylated, indicating that a noncatalytic function of Gcn5 is targeted by this suppressor protein. Reg1 protein is a major regulator of Snf1 kinase that phosphorylates Ser10 of histone H3. However, whereas Snf1 protein is important for HIS3 expression, replacing Ser10 of H3 with alanine or glutamate neither attenuates nor augments the BGR phenotypes. Overproduction of Snf1 protein also preferentially rescues the E173H allele. Biochemically, both Snf1 and Reg1(1-740) proteins copurify with Gcn5 protein. Snf1 can phosphorylate recombinant Gcn5 in vitro. Together, these data suggest that Reg1 and Snf1 proteins function in an H3 phosphorylation-independent pathway that also involves a noncatalytic role played by Gcn5 protein.
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Affiliation(s)
- Yang Liu
- 401 BCH Building, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824.
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20
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La Rue J, Tokarz S, Lanker S. SCFGrr1-mediated ubiquitination of Gis4 modulates glucose response in yeast. J Mol Biol 2005; 349:685-98. [PMID: 15890364 DOI: 10.1016/j.jmb.2005.03.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 03/22/2005] [Accepted: 03/23/2005] [Indexed: 11/21/2022]
Abstract
The F box protein Grr1 is the substrate specificity-determinant of the SCF(Grr1) E3 ubiquitin ligase complex. Genetic analyses of Grr1 mutants have implicated Grr1 in glucose repression, specifically with regard to expression of the SUC2 transcript. To better understand Grr1, we screened for substrates using a mutant version of Grr1 that should not associate with the SCF complex. We identified Gis4 as a novel Grr1 substrate. Gis4 was originally isolated as a multi-copy suppressor of a Gal--phenotype in the triple mutant snf1 mig1 srb8. Here, we show that Gis4 binds Grr1 in vivo and that Grr1 protein levels positively affect the protein levels of Gis4. The Gis4 protein is stable in wild-type cells and in grr1Delta cells; however, Gis4 is ubiquitinated in a Grr1-dependent manner. Furthermore, we show that Gis4 interacts with Snf1 in a Grr1-dependent fashion, and that Gis4 is involved in de-repression of SUC2 and in transcription of other Snf1-dependent transcripts. Gis4 appears to connect the glucose repression and de-repression pathways. We suggest that Gis4 may explain the glucose repression defects in carbon source metabolism for the grr1 mutants.
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Affiliation(s)
- Janna La Rue
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR 97239, USA
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21
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Ge D, Lamontagne B, Elela SA. RNase III-mediated silencing of a glucose-dependent repressor in yeast. Curr Biol 2005; 15:140-5. [PMID: 15668170 DOI: 10.1016/j.cub.2004.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Revised: 10/21/2004] [Accepted: 11/10/2004] [Indexed: 11/19/2022]
Abstract
Members of the RNase III family are found in all species examined with the exception of archaebacteria, where the functions of RNase III are carried out by the bulge-helix-bulge nuclease (BHB). In bacteria, RNase III contributes to the processing of many noncoding RNAs and directly cleaves several cellular and phage mRNAs. In eukaryotes, orthologs of RNase III participate in the biogenesis of many miRNAs and siRNAs, and this biogenesis initiates the degradation or translational repression of several mRNAs. However, the capacity of eukaryotic RNase IIIs to regulate gene expression by directly cleaving within the coding sequence of mRNAs remains speculative. Here we show that Rnt1p, a member of the RNase III family, selectively inhibits gene expression in baker's yeast by directly cleaving a stem-loop structure within the mRNA coding sequence. Analysis of mRNA expression upon the deletion of Rnt1p revealed an upregulation of the glucose-dependent repressor Mig2p. Mig2p mRNA became more stable upon the deletion of Rnt1p and resisted glucose-dependent degradation. In vitro, Rnt1p cleaved Mig2p mRNA and a silent mutation that disrupts Rnt1p signals blocked Mig2p mRNA degradation. These observations reveal a new RNase III-dependent mechanism of eukaryotic mRNA degradation.
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Affiliation(s)
- Dongling Ge
- Groupe ARN/RNA Group, Département de Microbiologie et d'Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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22
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Lascaris R, Piwowarski J, van der Spek H, de Mattos JT, Grivell L, Blom J. Overexpression of HAP4 in glucose-derepressed yeast cells reveals respiratory control of glucose-regulated genes. MICROBIOLOGY-SGM 2004; 150:929-934. [PMID: 15073302 DOI: 10.1099/mic.0.26742-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A link between control of respiration and glucose repression in yeast is reported. The HAP4 gene was overexpressed in a Delta mig1 deletion background, generating a mutant in which respiratory function is stimulated and glucose repression is diminished. Although this combination does not result in derepression of genes encoding proteins involved in respiratory function, it nevertheless generates resistance against 2-deoxyglucose and hence contributes to more derepressed growth characteristics. Unexpectedly, overexpression of HAP4 in the Delta mig1 deletion strain causes strong repression of several target genes of the Mig1p repressor. Repression is not restricted to glucose growth conditions and does not require the glucose repressors Mig2p or Hxk2p. It was observed that expression of the SUC2 gene is transiently repressed after glucose is added to respiratory-growing Delta mig1 cells. Additional overexpression of HAP4 prevents release from this novel repressed state. The data presented show that respiratory function controls transcription of genes required for the metabolism of alternative sugars. This respiratory feedback control is suggested to regulate the feed into glycolysis in derepressed conditions.
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Affiliation(s)
- Romeo Lascaris
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Jan Piwowarski
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Hans van der Spek
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Joost Teixeira de Mattos
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Les Grivell
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Jolanda Blom
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
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23
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Schüller HJ. Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae. Curr Genet 2003; 43:139-60. [PMID: 12715202 DOI: 10.1007/s00294-003-0381-8] [Citation(s) in RCA: 331] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2002] [Revised: 01/20/2003] [Accepted: 01/21/2003] [Indexed: 11/30/2022]
Abstract
Although sugars are clearly the preferred carbon sources of the yeast Saccharomyces cerevisiae, nonfermentable substrates such as ethanol, glycerol, lactate, acetate or oleate can also be used for the generation of energy and cellular biomass. Several regulatory networks of glucose repression (carbon catabolite repression) are involved in the coordinate biosynthesis of enzymes required for the utilization of nonfermentable substrates. Positively and negatively acting complexes of pleiotropic regulatory proteins have been characterized. The Snf1 (Cat1) protein kinase complex, together with its regulatory subunit Snf4 (Cat3) and alternative beta-subunits Sip1, Sip2 or Gal83, plays an outstanding role for the derepression of structural genes which are repressed in the presence of a high glucose concentration. One molecular function of the Snf1 complex is deactivation by phosphorylation of the general glucose repressor Mig1. In addition to regulation of alternative sugar fermentation, Mig1 also influences activators of respiration and gluconeogenesis, although to a lesser extent. Snf1 is also required for conversion of specific regulatory factors into transcriptional activators. This review summarizes regulatory cis-acting elements of structural genes of the nonfermentative metabolism, together with the corresponding DNA-binding proteins (Hap2-5, Rtg1-3, Cat8, Sip4, Adr1, Oaf1, Pip2), and describes the molecular interactions among general regulators and pathway-specific factors. In addition to the influence of the carbon source at the transcriptional level, mechanisms of post-transcriptional control such as glucose-regulated stability of mRNA are also discussed briefly.
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Affiliation(s)
- Hans-Joachim Schüller
- Institut für Mikrobiologie, Abteilung Genetik und Biochemie, Ernst-Moritz-Arndt-Universität, Jahnstrasse 15a, 17487 Greifswald, Germany.
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24
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Abstract
We used a biochemical genomics method of assaying Saccharomyces cerevisiae proteins, derived from a nearly complete set of glutathione S-transferase fusions, to develop an approach that is able to identify proteins that bind to a DNA element. Using the upstream activation sequence (UAS) of the promoter for the invertase gene, SUC2, we identified both specific and nonspecific binding activities, which could be classified based on whether they bound with equivalent affinity to a nonspecific DNA competitor. Three transcription factors, Mig1, Yer028c, and Rgt1, were found to be binding activities specific to the SUC2 UAS. Mig1 and Yer028c had been reported previously to bind to elements within the SUC2 UAS, validating the ability of the method to identify sequence-specific factors. The third activity, Rgt1, had not been reported previously to bind to SUC2. Additional gel shift assays narrowed the Rgt1 binding site to the SUC2-B element within the SUC2 UAS, which is similar to previously identified Rgt1 binding sites present in other genes. In vivo levels of invertase activity in an rgt1Delta strain were reduced relative to an isogenic RGT+ strain when these strains were grown under inducing (low glucose) conditions, suggesting that Rgt1 may have a role in the activated transcription of SUC2. This report demonstrates the feasibility of identifying DNA binding activities by rapidly assaying a large fraction of the predicted open reading frames of an organism for binding to a regulatory DNA motif.
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Affiliation(s)
- Tony R Hazbun
- Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
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25
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Zaragoza O, Vincent O, Gancedo JM. Regulatory elements in the FBP1 promoter respond differently to glucose-dependent signals in Saccharomyces cerevisiae. Biochem J 2001; 359:193-201. [PMID: 11563983 PMCID: PMC1222135 DOI: 10.1042/0264-6021:3590193] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In Saccharomyces cerevisiae expression of the fructose-1,6-bisphosphatase-encoding gene, FBP1, is controlled by glucose through the upstream activating sequences UAS1 and UAS2 and the upstream repressing sequence URS1 in its promoter. We have studied the regulation of the proteins that could bind to these elements. We have investigated the role of the putative transcription factors Cat8 and Sip4 in the formation of specific DNA-protein complexes with UAS1 and UAS2, and in the expression of UAS1-lacZ and UAS2-lacZ. The expression of CAT8-lacZ and SIP4-lacZ has been also measured in mig1, tup1 or hxk2 mutants, partially refractory to catabolite repression. We conclude that there is no strict correlation between Cat8 and Sip4 expression or in vitro formation of DNA-protein complexes and expression of UAS1-lacZ and UAS2-lacZ. The URS1 element binds the regulatory protein Mig1, which blocks transcription by recruiting the proteins Cyc8 and Tup1. The pattern of complexes of URS1 with nuclear extracts was dependent on the carbon source and on Cyc8, but not on Tup1; it was also affected by the protein kinase Snf1 and by the exportin Msn5. The repression caused by URS1 in a fusion gene was dependent on Mig1, Cyc8 and Tup1, and on the carbon source in the medium; in a snf1 strain the repression observed was independent of the carbon source. Expression of Mig1 could occur in the absence of Snf1 and was moderately sensitive to glucose. We present data showing that different elements of the regulatory system controlling FBP1 responded differently to the concentration of glucose in the medium.
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MESH Headings
- Basic-Leucine Zipper Transcription Factors
- Blotting, Northern
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/physiology
- Electrophoretic Mobility Shift Assay
- Fructose-Bisphosphatase
- Fungal Proteins/genetics
- Fungal Proteins/metabolism
- Gene Expression Regulation, Fungal/drug effects
- Gene Expression Regulation, Fungal/genetics
- Glucose/pharmacology
- Mutation/genetics
- Nuclear Proteins/physiology
- Promoter Regions, Genetic/drug effects
- Promoter Regions, Genetic/genetics
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Regulatory Sequences, Nucleic Acid/drug effects
- Regulatory Sequences, Nucleic Acid/genetics
- Regulatory Sequences, Nucleic Acid/physiology
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Repressor Proteins/physiology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Saccharomyces cerevisiae Proteins/physiology
- Trans-Activators/physiology
- Transcription Factors/physiology
- Transcription, Genetic
- Zinc Fingers
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Affiliation(s)
- O Zaragoza
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Arturo Duperier 4, E-28029 Madrid, Spain
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26
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Park S, Jeong HY, Kim HS, Yang MS, Chae KS. Enhanced production of Aspergillus ficuum endoinulinase in Saccharomyces cerevisiae by using the SUC2-deletion mutation. Enzyme Microb Technol 2001. [DOI: 10.1016/s0141-0229(01)00358-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Janoo RT, Neely LA, Braun BR, Whitehall SK, Hoffman CS. Transcriptional regulators of the Schizosaccharomyces pombe fbp1 gene include two redundant Tup1p-like corepressors and the CCAAT binding factor activation complex. Genetics 2001; 157:1205-15. [PMID: 11238405 PMCID: PMC1461578 DOI: 10.1093/genetics/157.3.1205] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Schizosaccharomyces pombe fbp1 gene, which encodes fructose-1,6-bis-phosphatase, is transcriptionally repressed by glucose through the activation of the cAMP-dependent protein kinase A (PKA) and transcriptionally activated by glucose starvation through the activation of a mitogen-activated protein kinase (MAPK). To identify transcriptional regulators acting downstream from or in parallel to PKA, we screened an adh-driven cDNA plasmid library for genes that increase fbp1 transcription in a strain with elevated PKA activity. Two such clones express amino-terminally truncated forms of the S. pombe tup12 protein that resembles the Saccharomyces cerevisiae Tup1p global corepressor. These clones appear to act as dominant negative alleles. Deletion of both tup12 and the closely related tup11 gene causes a 100-fold increase in fbp1-lacZ expression, indicating that tup11 and tup12 are redundant negative regulators of fbp1 transcription. In strains lacking tup11 and tup12, the atf1-pcr1 transcriptional activator continues to play a central role in fbp1-lacZ expression; however, spc1 MAPK phosphorylation of atf1 is no longer essential for its activation. We discuss possible models for the role of tup11- and tup12-mediated repression with respect to signaling from the MAPK and PKA pathways. A third clone identified in our screen expresses the php5 protein subunit of the CCAAT-binding factor (CBF). Deletion of php5 reduces fbp1 expression under both repressed and derepressed conditions. The CBF appears to act in parallel to atf1-pcr1, although it is unclear whether or not CBF activity is regulated by PKA.
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Affiliation(s)
- R T Janoo
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467, USA
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28
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Pascual-Ahuir A, Serrano R, Proft M. The Sko1p repressor and Gcn4p activator antagonistically modulate stress-regulated transcription in Saccharomyces cerevisiae. Mol Cell Biol 2001; 21:16-25. [PMID: 11113177 PMCID: PMC86564 DOI: 10.1128/mcb.21.1.16-25.2001] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the transcriptional response of Saccharomyces cerevisiae to stress, both activators and repressors are implicated. Here we demonstrate that the ion homeostasis determinant, HAL1, is regulated by two antagonistically operating bZIP transcription factors, the Sko1p repressor and the Gcn4p activator. A single CRE-like sequence (CRE(HAL1)) at position -222 to -215 with the palindromic core sequence TTACGTAA is essential for stress-induced expression of HAL1. Down-regulation of HAL1 under normal growth conditions requires specific binding of Sko1p to CRE(HAL1) and the corepressor gene SSN6. Release from this repression depends on the function of the high-osmolarity glycerol pathway. The Gcn4p transcriptional activator binds in vitro to the same CRE(HAL1) and is necessary for up-regulated HAL1 expression in vivo, indicating a dual control mechanism by a repressor-activator pair occupying the same promoter target sequence. gcn4 mutants display a strong sensitivity to elevated K(+) or Na(+) concentrations in the growth medium. In addition to reduced HAL1 expression, this sensitivity is explained by the fact that amino acid uptake is drastically impaired by high Na(+) and K(+) concentrations in wild-type yeast cells. The reduced amino acid biosynthesis of gcn4 mutants would result in amino acid deprivation. Together with the induction of HAL1 by amino acid starvation, these results suggest that salt stress and amino acid availability are physiologically interconnected.
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Affiliation(s)
- A Pascual-Ahuir
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, 46022 Valencia, Spain
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29
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Burke PV, Kwast KE. Oxygen dependence of expression of cytochrome C and cytochrome C oxidase genes in S. cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2000; 475:197-208. [PMID: 10849661 DOI: 10.1007/0-306-46825-5_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- P V Burke
- Department of Molecular and Integrative Physiology, University of Illinois, Urbana, USA
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30
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Abstract
Glucose transport and glycolysis are two sequential events which are regulated by both physiological and environmental signals in the yeast Saccharomyces cerevisiae. Transcription of the HXT4 gene was found to be regulated by Gcr1p and Gcr2p, transcription factors that are required for the regulated high level transcriptions of glycolytic genes. Transcription of HXT4 decreased about 35-fold in gcr1 mutant and two-fold in gcr2 mutant yeast cells. However, transcription of other HXT genes was not affected at a significant level by gcr1 or gcr2 mutations. Overproduction of Gcr1p from an inducible promoter resulted in a 15-64% increase in transcription of HXT4, depending on the growth conditions. Gel mobility shift assays performed with the purified DNA binding domain of Gcr1p and the UAS region of the HXT4 gene showed that Gcr1p interacts directly with multiple sites on the HXT4 UAS region. These results indicate that Gcr1p and Gcr2p coordinate the transcription of HXT4 and glycolytic genes.
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Affiliation(s)
- S Türkel
- Abant Izzet Baysal University, Faculty of Arts and Sciences, Department of Biology, 14280-Bolu, Turkey.
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31
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Abstract
The Snf1 protein kinase is a central component of the signaling pathway for glucose repression in yeast. Recent studies have addressed the regulation of Snf1 kinase activity and elucidated mechanisms by which Snf1 controls repression and activation of glucose-repressed genes. Important advances include evidence that Snf1 regulates the localization of the Mig1 repressor and that Snf1 functions at multiple points to control Cat8 and Sip4, the activators of gluconeogenic genes.
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Affiliation(s)
- M Carlson
- Departments of Genetics and Development and Microbiology, Columbia University, HHSC 922, Box 136, 701 W. 168th Street, New York, NY 10032, USA.
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Türkel S. Hyperosmotic stress represses the transcription of HXT2 and HXT4 genes in Saccharomyces cerevisiae. Folia Microbiol (Praha) 1999; 44:372-6. [PMID: 10983231 DOI: 10.1007/bf02903707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Effects of hyperosmotic stress on the transcriptional regulation of the HXT2 and HXT4 genes of Saccharomyces cerevisiae were investigated under glucose-repressed and -depressed growth conditions. Hyperosmotic stress repressed the transcription of these HXT genes up to 81% depending on growth conditions. Preconditioning of yeast cells for the hyperosmotic stress resulted in a much stronger repression of both HXT genes. The negative effect of hyperosmotic stress was much higher for HXT4 than HXT2. These results also show that hyperosmotic stress interferes with the glucose-dependent transcriptional activation or derepression of HXT2 and HXT4 genes transcription in S. cerevisiae.
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Affiliation(s)
- S Türkel
- Abant Izzet Baysal University, Faculty of Arts and Sciences, Department of Biology, Bolu, Turkey.
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