1
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Malla A, Gupta S, Sur R. Glycolytic enzymes in non-glycolytic web: functional analysis of the key players. Cell Biochem Biophys 2024; 82:351-378. [PMID: 38196050 DOI: 10.1007/s12013-023-01213-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/26/2023] [Indexed: 01/11/2024]
Abstract
To survive in the tumour microenvironment, cancer cells undergo rapid metabolic reprograming and adaptability. One of the key characteristics of cancer is increased glycolytic selectivity and decreased oxidative phosphorylation (OXPHOS). Apart from ATP synthesis, glycolysis is also responsible for NADH regeneration and macromolecular biosynthesis, such as amino acid biosynthesis and nucleotide biosynthesis. This allows cancer cells to survive and proliferate even in low-nutrient and oxygen conditions, making glycolytic enzymes a promising target for various anti-cancer agents. Oncogenic activation is also caused by the uncontrolled production and activity of glycolytic enzymes. Nevertheless, in addition to conventional glycolytic processes, some glycolytic enzymes are involved in non-canonical functions such as transcriptional regulation, autophagy, epigenetic changes, inflammation, various signaling cascades, redox regulation, oxidative stress, obesity and fatty acid metabolism, diabetes and neurodegenerative disorders, and hypoxia. The mechanisms underlying the non-canonical glycolytic enzyme activities are still not comprehensive. This review summarizes the current findings on the mechanisms fundamental to the non-glycolytic actions of glycolytic enzymes and their intermediates in maintaining the tumor microenvironment.
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Affiliation(s)
- Avirup Malla
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Suvroma Gupta
- Department of Aquaculture Management, Khejuri college, West Bengal, Baratala, India.
| | - Runa Sur
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.
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2
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Pérez-Díaz AJ, Vázquez-Marín B, Vicente-Soler J, Prieto-Ruiz F, Soto T, Franco A, Cansado J, Madrid M. cAMP-Protein kinase A and stress-activated MAP kinase signaling mediate transcriptional control of autophagy in fission yeast during glucose limitation or starvation. Autophagy 2023; 19:1311-1331. [PMID: 36107819 PMCID: PMC10012941 DOI: 10.1080/15548627.2022.2125204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022] Open
Abstract
Macroautophagy/autophagy is an essential adaptive physiological response in eukaryotes induced during nutrient starvation, including glucose, the primary immediate carbon and energy source for most cells. Although the molecular mechanisms that induce autophagy during glucose starvation have been extensively explored in the budding yeast Saccharomyces cerevisiae, little is known about how this coping response is regulated in the evolutionary distant fission yeast Schizosaccharomyces pombe. Here, we show that S. pombe autophagy in response to glucose limitation relies on mitochondrial respiration and the electron transport chain (ETC), but, in contrast to S. cerevisiae, the AMP-activated protein kinase (AMPK) and DNA damage response pathway components do not modulate fission yeast autophagic flux under these conditions. In the presence of glucose, the cAMP-protein kinase A (PKA) signaling pathway constitutively represses S. pombe autophagy by downregulating the transcription factor Rst2, which promotes the expression of respiratory genes required for autophagy induction under limited glucose availability. Furthermore, the stress-activated protein kinase (SAPK) signaling pathway, and its central mitogen-activated protein kinase (MAPK) Sty1, positively modulate autophagy upon glucose limitation at the transcriptional level through its downstream effector Atf1 and by direct in vivo phosphorylation of Rst2 at S292. Thus, our data indicate that the signaling pathways that govern autophagy during glucose shortage or starvation have evolved differently in S. pombe and uncover the existence of sophisticated and multifaceted mechanisms that control this self-preservation and survival response.
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Affiliation(s)
- Armando Jesús Pérez-Díaz
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Beatriz Vázquez-Marín
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Jero Vicente-Soler
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Francisco Prieto-Ruiz
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Teresa Soto
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Alejandro Franco
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - José Cansado
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Marisa Madrid
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
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3
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Tup1 is critical for transcriptional repression in Quiescence in S. cerevisiae. PLoS Genet 2022; 18:e1010559. [PMID: 36542663 DOI: 10.1371/journal.pgen.1010559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/05/2023] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Upon glucose starvation, S. cerevisiae shows a dramatic alteration in transcription, resulting in wide-scale repression of most genes and activation of some others. This coincides with an arrest of cellular proliferation. A subset of such cells enters quiescence, a reversible non-dividing state. Here, we demonstrate that the conserved transcriptional corepressor Tup1 is critical for transcriptional repression after glucose depletion. We show that Tup1-Ssn6 binds new targets upon glucose depletion, where it remains as the cells enter the G0 phase of the cell cycle. In addition, we show that Tup1 represses a variety of glucose metabolism and transport genes. We explored how Tup1 mediated repression is accomplished and demonstrated that Tup1 coordinates with the Rpd3L complex to deacetylate H3K23. We found that Tup1 coordinates with Isw2 to affect nucleosome positions at glucose transporter HXT family genes during G0. Finally, microscopy revealed that a quarter of cells with a Tup1 deletion contain multiple DAPI puncta. Taken together, these findings demonstrate the role of Tup1 in transcriptional reprogramming in response to environmental cues leading to the quiescent state.
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4
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2-deoxyglucose transiently inhibits yeast AMPK signaling and triggers glucose transporter endocytosis, potentiating the drug toxicity. PLoS Genet 2022; 18:e1010169. [PMID: 35951639 PMCID: PMC9398028 DOI: 10.1371/journal.pgen.1010169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/23/2022] [Accepted: 07/20/2022] [Indexed: 11/19/2022] Open
Abstract
2-deoxyglucose is a glucose analog that impacts many aspects of cellular physiology. After its uptake and its phosphorylation into 2-deoxyglucose-6-phosphate (2DG6P), it interferes with several metabolic pathways including glycolysis and protein N-glycosylation. Despite this systemic effect, resistance can arise through strategies that are only partially understood. In yeast, 2DG resistance is often associated with mutations causing increased activity of the yeast 5’-AMP activated protein kinase (AMPK), Snf1. Here we focus on the contribution of a Snf1 substrate in 2DG resistance, namely the alpha-arrestin Rod1 involved in nutrient transporter endocytosis. We report that 2DG triggers the endocytosis of many plasma membrane proteins, mostly in a Rod1-dependent manner. Rod1 participates in 2DG-induced endocytosis because 2DG, following its phosphorylation by hexokinase Hxk2, triggers changes in Rod1 post-translational modifications and promotes its function in endocytosis. Mechanistically, this is explained by a transient, 2DG-induced inactivation of Snf1/AMPK by protein phosphatase 1 (PP1). We show that 2DG-induced endocytosis is detrimental to cells, and the lack of Rod1 counteracts this process by stabilizing glucose transporters at the plasma membrane. This facilitates glucose uptake, which may help override the metabolic blockade caused by 2DG, and 2DG export—thus terminating the process of 2DG detoxification. Altogether, these results shed a new light on the regulation of AMPK signaling in yeast and highlight a remarkable strategy to bypass 2DG toxicity involving glucose transporter regulation.
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5
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Ma X, Jiang Y, Ma L, Luo S, Du H, Li X, Xing F. Corepressors SsnF and RcoA Regulate Development and Aflatoxin B1 Biosynthesis in Aspergillus flavus NRRL 3357. Toxins (Basel) 2022; 14:toxins14030174. [PMID: 35324671 PMCID: PMC8954095 DOI: 10.3390/toxins14030174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023] Open
Abstract
Aspergillus flavus is a saprophytic fungus that can be found across the entire world. It can produce aflatoxin B1 (AFB1), which threatens human health. CreA, as the central factor in carbon catabolite repression (CCR), regulates carbon catabolism and AFB1 biosynthesis in A. flavus. Additionally, SsnF-RcoA are recognized as the corepressors of CreA in CCR. In this study, ssnF and rcoA not only regulated the expressions of CCR factors and hydrolase genes, but also positively affected mycelia growth, conidia production, sclerotia formation, and osmotic stress response in A. flavus. More importantly, SsnF and RcoA were identified as positive regulators for AFB1 biosynthesis, as they modulate the AF cluster genes and the relevant regulators at a transcriptional level. Additionally, the interactions of SsnF-CreA and RcoA-CreA were strong and moderate, respectively. However, the interaction of SsnF and RcoA was weak. The interaction models of CreA-SsnF, CreA-RcoA, and SsnF-RcoA were also simulated with a docking analysis. All things considered, SsnF and RcoA are not just the critical regulators of the CCR pathway, but the global regulators involving in morphological development and AFB1 biosynthesis in A. flavus.
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Affiliation(s)
| | | | | | | | | | - Xu Li
- Correspondence: (X.L.); (F.X.)
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6
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Muñoz-Miranda LA, Pereira-Santana A, Gómez-Angulo JH, Gschaedler-Mathis AC, Amaya-Delgado L, Figueroa-Yáñez LJ, Arrizon J. Identification of genes related to hydrolysis and assimilation of Agave fructans in Candida apicola NRRL Y-50540 and Torulaspora delbrueckii NRRL Y-50541 by de
novo transcriptome analysis. FEMS Yeast Res 2022; 22. [DOI: 10.1093/femsyr/foac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
Abstract
Fructans are the main sugar in agave pine used by yeasts during mezcal fermentation processes, from which Candida apicola NRRL Y-50540 and Torulaspora delbrueckii NRRL Y-50541 were isolated. De novo transcriptome analysis was carried out to identify genes involved in the hydrolysis and assimilation of Agave fructans (AF). We identified a transcript annotated as SUC2, which is related to β-fructofuranosidase activity, and several differential expressed genes involved in the transcriptional regulation of SUC2 such as: MIG1, MTH1, SNF1, SNF5, REG1, SSN6, SIP1, SIP2, SIP5, GPR1, RAS2, and PKA. Some of these genes were specifically expressed in some of the yeasts according to their fructans assimilation metabolism. Different hexose transporters that could be related to the assimilation of fructose and glucose were found in both the transcriptomes. Our findings provide a better understanding of AF assimilation in these yeasts and provide resources for further metabolic engineering and biotechnology applications.
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Affiliation(s)
- Luis A Muñoz-Miranda
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. División de Biotecnología Industrial, Zapopan, Jalisco, 45019, México
| | - Alejandro Pereira-Santana
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. División de Biotecnología Industrial, Zapopan, Jalisco, 45019, México
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, 03940, México
| | - Jorge H Gómez-Angulo
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. División de Biotecnología Industrial, Zapopan, Jalisco, 45019, México
- Centro Universitario de Ciencias Exactas e Ingenierías (UDG), Departamento de Ingeniería Química, Guadalajara, Jalisco, 44430, México
| | - Anne Christine Gschaedler-Mathis
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. División de Biotecnología Industrial, Zapopan, Jalisco, 45019, México
| | - Lorena Amaya-Delgado
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. División de Biotecnología Industrial, Zapopan, Jalisco, 45019, México
| | - Luis J Figueroa-Yáñez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. División de Biotecnología Industrial, Zapopan, Jalisco, 45019, México
| | - Javier Arrizon
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. División de Biotecnología Industrial, Zapopan, Jalisco, 45019, México
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7
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Sasaki Y, Yoshikuni Y. Metabolic engineering for valorization of macroalgae biomass. Metab Eng 2022; 71:42-61. [PMID: 35077903 DOI: 10.1016/j.ymben.2022.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/18/2022]
Abstract
Marine macroalgae have huge potential as feedstocks for production of a wide spectrum of chemicals used in biofuels, biomaterials, and bioactive compounds. Harnessing macroalgae in these ways could promote wellbeing for people while mitigating climate change and environmental destruction linked to use of fossil fuels. Microorganisms play pivotal roles in converting macroalgae into valuable products, and metabolic engineering technologies have been developed to extend their native capabilities. This review showcases current achievements in engineering the metabolisms of various microbial chassis to convert red, green, and brown macroalgae into bioproducts. Unique features of macroalgae, such as seasonal variation in carbohydrate content and salinity, provide the next challenges to advancing macroalgae-based biorefineries. Three emerging engineering strategies are discussed here: (1) designing dynamic control of metabolic pathways, (2) engineering strains of halophilic (salt-tolerant) microbes, and (3) developing microbial consortia for conversion. This review illuminates opportunities for future research communities by elucidating current approaches to engineering microbes so they can become cell factories for the utilization of macroalgae feedstocks.
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Affiliation(s)
- Yusuke Sasaki
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, 060-8589, Japan.
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8
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Lettow J, Aref R, Schüller HJ. Transcriptional repressor Gal80 recruits corepressor complex Cyc8-Tup1 to structural genes of the Saccharomyces cerevisiae GAL regulon. Curr Genet 2021; 68:115-124. [PMID: 34622331 PMCID: PMC8801411 DOI: 10.1007/s00294-021-01215-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/14/2021] [Accepted: 09/26/2021] [Indexed: 11/30/2022]
Abstract
Under non-inducing conditions (absence of galactose), yeast structural genes of the GAL regulon are repressed by Gal80, preventing interaction of Gal4 bound to UASGAL promoter motifs with general factors of the transcriptional machinery. In this work, we show that Gal80 is also able to interact with histone deacetylase-recruiting corepressor proteins Cyc8 and Tup1, indicating an additional mechanism of gene repression. This is supported by our demonstration that a lexA–Gal80 fusion efficiently mediates repression of a reporter gene with an upstream lexA operator sequence. Corepressor interaction and in vivo gene repression could be mapped to a Gal80 minimal domain of 65 amino acids (aa 81-145). Site-directed mutagenesis of selected residues within this domain showed that a cluster of aromatic-hydrophobic amino acids (YLFV, aa 118-121) is important, although not solely responsible, for gene repression. Using chromatin immunoprecipitation, Cyc8 and Tup1 were shown to be present at the GAL1 promoter in a wild-type strain but not in a gal80 mutant strain under non-inducing (derepressing) growth conditions. Expression of a GAL1–lacZ fusion was elevated in a tup1 mutant (but not in a cyc8 mutant) grown in derepressing medium, indicating that Tup1 may be mainly responsible for this second mechanism of Gal80-dependent gene repression.
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Affiliation(s)
- Julia Lettow
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Felix-Hausdorff-Str. 8, 17487, Greifswald, Germany
| | - Rasha Aref
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Shoubra El-Khaymah, Cairo, 11241, Egypt
| | - Hans-Joachim Schüller
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Felix-Hausdorff-Str. 8, 17487, Greifswald, Germany.
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9
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Parnell EJ, Parnell TJ, Stillman DJ. Genetic analysis argues for a coactivator function for the Saccharomyces cerevisiae Tup1 corepressor. Genetics 2021; 219:6329640. [PMID: 34849878 DOI: 10.1093/genetics/iyab120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/20/2021] [Indexed: 11/14/2022] Open
Abstract
The Tup1-Cyc8 corepressor complex of Saccharomyces cerevisiae is recruited to promoters by DNA-binding proteins to repress transcription of genes, including the a-specific mating-type genes. We report here a tup1(S649F) mutant that displays mating irregularities and an α-predominant growth defect. RNA-Seq and ChIP-Seq were used to analyze gene expression and Tup1 occupancy changes in mutant vs wild type in both a and α cells. Increased Tup1(S649F) occupancy tended to occur upstream of upregulated genes, whereas locations with decreased occupancy usually did not show changes in gene expression, suggesting this mutant not only loses corepressor function but also behaves as a coactivator. Based upon studies demonstrating a dual role of Tup1 in both repression and activation, we postulate that the coactivator function of Tup1(S649F) results from diminished interaction with repressor proteins, including α2. We also found that large changes in mating-type-specific gene expression between a and α or between mutant and wild type were not easily explained by the range of Tup1 occupancy levels within their promoters, as predicted by the classic model of a-specific gene repression by Tup1. Most surprisingly, we observed Tup1 occupancy upstream of the a-specific gene MFA2 and the α-specific gene MF(ALPHA)1 in cells in which each gene was expressed rather than repressed. These results, combined with the identification of additional mating-related genes upregulated in the tup1(S649F) α strain, illustrate that the role of Tup1 in distinguishing mating types in yeast appears to be both more comprehensive and more nuanced than previously appreciated.
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Affiliation(s)
- Emily J Parnell
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Timothy J Parnell
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - David J Stillman
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
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10
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Salsaa M, Aziz K, Lazcano P, Schmidtke MW, Tarsio M, Hüttemann M, Reynolds CA, Kane PM, Greenberg ML. Valproate activates the Snf1 kinase in Saccharomyces cerevisiae by decreasing the cytosolic pH. J Biol Chem 2021; 297:101110. [PMID: 34428448 PMCID: PMC8449051 DOI: 10.1016/j.jbc.2021.101110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022] Open
Abstract
Valproate (VPA) is a widely used mood stabilizer, but its therapeutic mechanism of action is not understood. This knowledge gap hinders the development of more effective drugs with fewer side effects. Using the yeast model to elucidate the effects of VPA on cellular metabolism, we determined that the drug upregulated expression of genes normally repressed during logarithmic growth on glucose medium and increased levels of activated (phosphorylated) Snf1 kinase, the major metabolic regulator of these genes. VPA also decreased the cytosolic pH (pHc) and reduced glycolytic production of 2/3-phosphoglycerate. ATP levels and mitochondrial membrane potential were increased, and glucose-mediated extracellular acidification decreased in the presence of the drug, as indicated by a smaller glucose-induced shift in pH, suggesting that the major P-type proton pump Pma1 was inhibited. Interestingly, decreasing the pHc by omeprazole-mediated inhibition of Pma1 led to Snf1 activation. We propose a model whereby VPA lowers the pHc causing a decrease in glycolytic flux. In response, Pma1 is inhibited and Snf1 is activated, resulting in increased expression of normally repressed metabolic genes. These findings suggest a central role for pHc in regulating the metabolic program of yeast cells.
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Affiliation(s)
- Michael Salsaa
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Kerestin Aziz
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Pablo Lazcano
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Michael W Schmidtke
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Maureen Tarsio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Christian A Reynolds
- Department of Emergency Medicine, School of Medicine, Wayne State University, Detroit, Michigan, USA; Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA.
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11
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Zhou X, Li J, Tang N, Xie H, Fan X, Chen H, Tang M, Xie X. Genome-Wide Analysis of Nutrient Signaling Pathways Conserved in Arbuscular Mycorrhizal Fungi. Microorganisms 2021; 9:1557. [PMID: 34442636 PMCID: PMC8401276 DOI: 10.3390/microorganisms9081557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/03/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi form a mutualistic symbiosis with a majority of terrestrial vascular plants. To achieve an efficient nutrient trade with their hosts, AM fungi sense external and internal nutrients, and integrate different hierarchic regulations to optimize nutrient acquisition and homeostasis during mycorrhization. However, the underlying molecular networks in AM fungi orchestrating the nutrient sensing and signaling remain elusive. Based on homology search, we here found that at least 72 gene components involved in four nutrient sensing and signaling pathways, including cAMP-dependent protein kinase A (cAMP-PKA), sucrose non-fermenting 1 (SNF1) protein kinase, target of rapamycin kinase (TOR) and phosphate (PHO) signaling cascades, are well conserved in AM fungi. Based on the knowledge known in model yeast and filamentous fungi, we outlined the possible gene networks functioning in AM fungi. These pathways may regulate the expression of downstream genes involved in nutrient transport, lipid metabolism, trehalase activity, stress resistance and autophagy. The RNA-seq analysis and qRT-PCR results of some core genes further indicate that these pathways may play important roles in spore germination, appressorium formation, arbuscule longevity and sporulation of AM fungi. We hope to inspire further studies on the roles of these candidate genes involved in these nutrient sensing and signaling pathways in AM fungi and AM symbiosis.
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Affiliation(s)
- Xiaoqin Zhou
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Jiangyong Li
- Institute for Environmental and Climate Research, Jinan University, Guangzhou 511443, China;
| | - Nianwu Tang
- UMR Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280 Champenoux, France;
| | - Hongyun Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xiaoning Fan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (H.X.); (X.F.); (H.C.)
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12
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Yang X, Meng L, Lin X, Jiang HY, Hu XP, Li CF. Role of Elm1, Tos3, and Sak1 Protein Kinases in the Maltose Metabolism of Baker's Yeast. Front Microbiol 2021; 12:665261. [PMID: 34140941 PMCID: PMC8204090 DOI: 10.3389/fmicb.2021.665261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/23/2021] [Indexed: 11/25/2022] Open
Abstract
Glucose repression is a key regulatory system controlling the metabolism of non-glucose carbon source in yeast. Glucose represses the utilization of maltose, the most abundant fermentable sugar in lean dough and wort, thereby negatively affecting the fermentation efficiency and product quality of pasta products and beer. In this study, the focus was on the role of three kinases, Elm1, Tos3, and Sak1, in the maltose metabolism of baker’s yeast in lean dough. The results suggested that the three kinases played different roles in the regulation of the maltose metabolism of baker’s yeast with differential regulations on MAL genes. Elm1 was necessary for the maltose metabolism of baker’s yeast in maltose and maltose-glucose, and the overexpression of ELM1 could enhance the maltose metabolism and lean dough fermentation ability by upregulating the transcription of MALx1 (x is the locus) in maltose and maltose-glucose and MALx2 in maltose. The native level of TOS3 and SAK1 was essential for yeast cells to adapt glucose repression, but the overexpression of TOS3 and SAK1 alone repressed the expression of MALx1 in maltose-glucose and MALx2 in maltose. Moreover, the three kinases might regulate the maltose metabolism via the Snf1-parallel pathways with a carbon source-dependent manner. These results, for the first time, suggested that Elm1, rather than Tos3 and Sak1, might be the dominant regulator in the maltose metabolism of baker’s yeast. These findings provided knowledge about the glucose repression of maltose and gave a new perspective for breeding industrial yeasts with rapid maltose metabolism.
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Affiliation(s)
- Xu Yang
- College of Food Science and Engineering, Hainan University, Haikou, China
| | - Lu Meng
- College of Food Science and Engineering, Hainan University, Haikou, China
| | - Xue Lin
- College of Food Science and Engineering, Hainan University, Haikou, China.,Engineering Research Center of Utilization of Tropical Polysaccharide Resources, Ministry of Education, Haikou, China.,Hainan Key Laboratory of Food Nutrition and Functional Food, Haikou, China
| | - Huan-Yuan Jiang
- College of Food Science and Engineering, Hainan University, Haikou, China
| | - Xiao-Ping Hu
- College of Food Science and Engineering, Hainan University, Haikou, China.,Engineering Research Center of Utilization of Tropical Polysaccharide Resources, Ministry of Education, Haikou, China.,Hainan Key Laboratory of Food Nutrition and Functional Food, Haikou, China
| | - Cong-Fa Li
- College of Food Science and Engineering, Hainan University, Haikou, China.,Engineering Research Center of Utilization of Tropical Polysaccharide Resources, Ministry of Education, Haikou, China.,Hainan Key Laboratory of Food Nutrition and Functional Food, Haikou, China
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13
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Auboiron M, Vasseur P, Tonazzini S, Fall A, Castro FR, Sučec I, El Koulali K, Urbach S, Radman-Livaja M. TrIPP-a method for tracking the inheritance patterns of proteins in living cells-reveals retention of Tup1p, Fpr4p, and Rpd3L in the mother cell. iScience 2021; 24:102075. [PMID: 33644711 PMCID: PMC7889982 DOI: 10.1016/j.isci.2021.102075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/27/2020] [Accepted: 01/15/2021] [Indexed: 01/16/2023] Open
Abstract
Inheritance of chromatin-bound proteins theoretically plays a role in the epigenetic transmission of cellular phenotypes. Protein segregation during cell division is however poorly understood. We now describe TrIPP (Tracking the Inheritance Patterns of Proteins): a live cell imaging method for tracking maternal proteins during asymmetric cell divisions of budding yeast. Our analysis of the partitioning pattern of a test set of 18 chromatin-associated proteins reveals that abundant and moderately abundant maternal proteins segregate stochastically and symmetrically between the two cells with the exception of Rxt3p, Fpr4p, and Tup1p, which are preferentially retained in the mother. Low abundance proteins also tend to be retained in the mother cell with the exception of Sir2p and the linker histone H1. Our analysis of chromatin protein behavior in single cells reveals potentially general trends such as coupled protein synthesis and decay and a correlation between protein half-lives and cell-cycle duration.
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Affiliation(s)
- Morgane Auboiron
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Pauline Vasseur
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Saphia Tonazzini
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Arame Fall
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Francesc Rubert Castro
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Iva Sučec
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Khadija El Koulali
- Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France.,Functional Proteomics Platform, IGF _ CNRS INSERM, Université de Montpellier, 141 rue de la Cardonille, 34094 Montpellier cedex 5, France
| | - Serge Urbach
- Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France.,Functional Proteomics Platform, IGF _ CNRS INSERM, Université de Montpellier, 141 rue de la Cardonille, 34094 Montpellier cedex 5, France
| | - Marta Radman-Livaja
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
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14
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The regulation of Saccharomyces cerevisiae Snf1 protein kinase on glucose utilization is in a glucose-dependent manner. Curr Genet 2021; 67:245-248. [PMID: 33385241 DOI: 10.1007/s00294-020-01137-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 01/13/2023]
Abstract
Protein phosphorylation catalyzed by protein kinases is the major regulatory mechanism that controls many cellular processes. The regulatory mechanism of one protein kinase in different signals is distinguished, probably inducing multiple phenotypes. The Saccharomyces cerevisiae Snf1 protein kinase, a member of the AMP‑activated protein kinase family, plays important roles in the response to nutrition and environmental stresses. Glucose is an important nutrient for life activities of cells, but glucose repression and osmotic pressure could be produced at certain concentrations. To deeply understand the role of Snf1 in the regulation of nutrient metabolism and stress response of S. cerevisiae cells, the role and the regulatory mechanism of Snf1 in glucose metabolism are discussed in different level of glucose: below 1% (glucose derepression status), in 2% (glucose repression status), and in 30% glucose (1.66 M, an osmotic equivalent to 0.83 M NaCl). In summary, Snf1 regulates glucose metabolism in a glucose-dependent manner, which is associated with the different regulation on activation, localization, and signal pathways of Snf1 by varied glucose. Exploring the regulatory mechanism of Snf1 in glucose metabolism in different concentrations of glucose can provide insights into the study of the global regulatory mechanism of Snf1 in yeast and can help to better understand the complexity of physiological response of cells to stresses.
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15
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Oh S, Lee J, Swanson SK, Florens L, Washburn MP, Workman JL. Yeast Nuak1 phosphorylates histone H3 threonine 11 in low glucose stress by the cooperation of AMPK and CK2 signaling. eLife 2020; 9:e64588. [PMID: 33372657 PMCID: PMC7781599 DOI: 10.7554/elife.64588] [Citation(s) in RCA: 4] [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: 11/03/2020] [Accepted: 12/26/2020] [Indexed: 12/26/2022] Open
Abstract
Changes in available nutrients are inevitable events for most living organisms. Upon nutritional stress, several signaling pathways cooperate to change the transcription program through chromatin regulation to rewire cellular metabolism. In budding yeast, histone H3 threonine 11 phosphorylation (H3pT11) acts as a marker of low glucose stress and regulates the transcription of nutritional stress-responsive genes. Understanding how this histone modification 'senses' external glucose changes remains elusive. Here, we show that Tda1, the yeast ortholog of human Nuak1, is a direct kinase for H3pT11 upon low glucose stress. Yeast AMP-activated protein kinase (AMPK) directly phosphorylates Tda1 to govern Tda1 activity, while CK2 regulates Tda1 nuclear localization. Collectively, AMPK and CK2 signaling converge on histone kinase Tda1 to link external low glucose stress to chromatin regulation.
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Affiliation(s)
- Seunghee Oh
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Jaehyoun Lee
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | | | - Michael P Washburn
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Pathology and Laboratory Medicine, University of Kansas Medical CenterKansas CityUnited States
| | - Jerry L Workman
- Stowers Institute for Medical ResearchKansas CityUnited States
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16
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Snf1 AMPK positively regulates ER-phagy via expression control of Atg39 autophagy receptor in yeast ER stress response. PLoS Genet 2020; 16:e1009053. [PMID: 32986716 PMCID: PMC7544123 DOI: 10.1371/journal.pgen.1009053] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/08/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022] Open
Abstract
Autophagy is a fundamental process responsible for degradation and recycling of intracellular contents. In the budding yeast, non-selective macroautophagy and microautophagy of the endoplasmic reticulum (ER) are caused by ER stress, the circumstance where aberrant proteins accumulate in the ER. The more recent study showed that protein aggregation in the ER initiates ER-selective macroautophagy, referred to as ER-phagy; however, the mechanisms by which ER stress induces ER-phagy have not been fully elucidated. Here, we show that the expression levels of ATG39, encoding an autophagy receptor specific for ER-phagy, are significantly increased under ER-stressed conditions. ATG39 upregulation in ER stress response is mediated by activation of its promoter, which is positively regulated by Snf1 AMP-activated protein kinase (AMPK) and negatively by Mig1 and Mig2 transcriptional repressors. In response to ER stress, Snf1 promotes nuclear export of Mig1 and Mig2. Our results suggest that during ER stress response, Snf1 mediates activation of the ATG39 promoter and consequently facilitates ER-phagy by negatively regulating Mig1 and Mig2.
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17
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González A, Hall MN, Lin SC, Hardie DG. AMPK and TOR: The Yin and Yang of Cellular Nutrient Sensing and Growth Control. Cell Metab 2020; 31:472-492. [PMID: 32130880 DOI: 10.1016/j.cmet.2020.01.015] [Citation(s) in RCA: 418] [Impact Index Per Article: 104.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The AMPK (AMP-activated protein kinase) and TOR (target-of-rapamycin) pathways are interlinked, opposing signaling pathways involved in sensing availability of nutrients and energy and regulation of cell growth. AMPK (Yin, or the "dark side") is switched on by lack of energy or nutrients and inhibits cell growth, while TOR (Yang, or the "bright side") is switched on by nutrient availability and promotes cell growth. Genes encoding the AMPK and TOR complexes are found in almost all eukaryotes, suggesting that these pathways arose very early during eukaryotic evolution. During the development of multicellularity, an additional tier of cell-extrinsic growth control arose that is mediated by growth factors, but these often act by modulating nutrient uptake so that AMPK and TOR remain the underlying regulators of cellular growth control. In this review, we discuss the evolution, structure, and regulation of the AMPK and TOR pathways and the complex mechanisms by which they interact.
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Affiliation(s)
- Asier González
- Biozentrum, University of Basel, CH4056 Basel, Switzerland
| | - Michael N Hall
- Biozentrum, University of Basel, CH4056 Basel, Switzerland
| | - Sheng-Cai Lin
- School of Life Sciences, Xiamen University, Xiamen, 361102 Fujian, China
| | - D Grahame Hardie
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK.
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18
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Guaragnella N, Coyne LP, Chen XJ, Giannattasio S. Mitochondria-cytosol-nucleus crosstalk: learning from Saccharomyces cerevisiae. FEMS Yeast Res 2019; 18:5066171. [PMID: 30165482 DOI: 10.1093/femsyr/foy088] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/02/2018] [Indexed: 12/16/2022] Open
Abstract
Mitochondria are key cell organelles with a prominent role in both energetic metabolism and the maintenance of cellular homeostasis. Since mitochondria harbor their own genome, which encodes a limited number of proteins critical for oxidative phosphorylation and protein translation, their function and biogenesis strictly depend upon nuclear control. The yeast Saccharomyces cerevisiae has been a unique model for understanding mitochondrial DNA organization and inheritance as well as for deciphering the process of assembly of mitochondrial components. In the last three decades, yeast also provided a powerful tool for unveiling the communication network that coordinates the functions of the nucleus, the cytosol and mitochondria. This crosstalk regulates how cells respond to extra- and intracellular changes either to maintain cellular homeostasis or to activate cell death. This review is focused on the key pathways that mediate nucleus-cytosol-mitochondria communications through both transcriptional regulation and proteostatic signaling. We aim to highlight yeast that likely continues to serve as a productive model organism for mitochondrial research in the years to come.
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Affiliation(s)
- Nicoletta Guaragnella
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 165/A, 70126 Bari, Italy
| | - Liam P Coyne
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Xin Jie Chen
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Sergio Giannattasio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 165/A, 70126 Bari, Italy
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19
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Vassiliadis D, Wong KH, Andrianopoulos A, Monahan BJ. A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe. BMC Genomics 2019; 20:251. [PMID: 30922219 PMCID: PMC6440086 DOI: 10.1186/s12864-019-5602-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/12/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Optimal glucose metabolism is central to the growth and development of cells. In microbial eukaryotes, carbon catabolite repression (CCR) mediates the preferential utilization of glucose, primarily by repressing alternate carbon source utilization. In fission yeast, CCR is mediated by transcriptional repressors Scr1 and the Tup/Ssn6 complex, with the Rst2 transcription factor important for activation of gluconeogenesis and sexual differentiation genes upon derepression. Through genetic and genome-wide methods, this study aimed to comprehensively characterize CCR in fission yeast by identifying the genes and biological processes that are regulated by Scr1, Tup/Ssn6 and Rst2, the core CCR machinery. RESULTS The transcriptional response of fission yeast to glucose-sufficient or glucose-deficient growth conditions in wild type and CCR mutant cells was determined by RNA-seq and ChIP-seq. Scr1 was found to regulate genes involved in carbon metabolism, hexose uptake, gluconeogenesis and the TCA cycle. Surprisingly, a role for Scr1 in the suppression of sexual differentiation was also identified, as homothallic scr1 deletion mutants showed ectopic meiosis in carbon and nitrogen rich conditions. ChIP-seq characterised the targets of Tup/Ssn6 and Rst2 identifying regulatory roles within and independent of CCR. Finally, a subset of genes bound by all three factors was identified, implying that regulation of certain loci may be modulated in a competitive fashion between the Scr1, Tup/Ssn6 repressors and the Rst2 activator. CONCLUSIONS By identifying the genes directly and indirectly regulated by Scr1, Tup/Ssn6 and Rst2, this study comprehensively defined the gene regulatory networks of CCR in fission yeast and revealed the transcriptional complexities governing this system.
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Affiliation(s)
- Dane Vassiliadis
- Genetics, Genomics & Systems Biology, School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia. .,Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, Australia.
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau, China.,Institute of Translational Medicine, University of Macau, Macau, China
| | - Alex Andrianopoulos
- Genetics, Genomics & Systems Biology, School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Brendon J Monahan
- Genetics, Genomics & Systems Biology, School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia. .,Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, Australia. .,Cancer Therapeutics (CTx), Parkville, Victoria, Australia.
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20
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Coccetti P, Nicastro R, Tripodi F. Conventional and emerging roles of the energy sensor Snf1/AMPK in Saccharomyces cerevisiae. MICROBIAL CELL 2018; 5:482-494. [PMID: 30483520 PMCID: PMC6244292 DOI: 10.15698/mic2018.11.655] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
All proliferating cells need to match metabolism, growth and cell cycle progression with nutrient availability to guarantee cell viability in spite of a changing environment. In yeast, a signaling pathway centered on the effector kinase Snf1 is required to adapt to nutrient limitation and to utilize alternative carbon sources, such as sucrose and ethanol. Snf1 shares evolutionary conserved functions with the AMP-activated Kinase (AMPK) in higher eukaryotes which, activated by energy depletion, stimulates catabolic processes and, at the same time, inhibits anabolism. Although the yeast Snf1 is best known for its role in responding to a number of stress factors, in addition to glucose limitation, new unconventional roles of Snf1 have recently emerged, even in glucose repressing and unstressed conditions. Here, we review and integrate available data on conventional and non-conventional functions of Snf1 to better understand the complexity of cellular physiology which controls energy homeostasis.
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Affiliation(s)
- Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Raffaele Nicastro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,Present address: Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,SYSBIO, Centre of Systems Biology, Milan, Italy
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21
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Lin X, Zhang CY, Meng L, Bai XW, Xiao DG. Overexpression of SNF4 and deletions of REG1- and REG2-enhanced maltose metabolism and leavening ability of baker's yeast in lean dough. J Ind Microbiol Biotechnol 2018; 45:827-838. [PMID: 29936578 DOI: 10.1007/s10295-018-2058-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/18/2018] [Indexed: 01/07/2023]
Abstract
Maltose metabolism of baker's yeast (Saccharomyces cerevisiae) in lean dough is suppressed by the glucose effect, which negatively affects dough fermentation. In this study, differences and interactions among SNF4 (encoding for the regulatory subunit of Snf1 kinase) overexpression and REG1 and REG2 (which encodes for the regulatory subunits of the type I protein phosphatase) deletions in maltose metabolism of baker's yeast were investigated using various mutants. Results revealed that SNF4 overexpression and REG1 and REG2 deletions effectively alleviated glucose repression at different levels, thereby enhancing maltose metabolism and leavening ability to varying degrees. SNF4 overexpression combined with REG1/REG2 deletions further enhanced the increases in glucose derepression and maltose metabolism. The overexpressed SNF4 with deleted REG1 and REG2 mutant ΔREG1ΔREG2 + SNF4 displayed the highest maltose metabolism and strongest leavening ability under the test conditions. Such baker's yeast strains had excellent potential applications.
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Affiliation(s)
- Xue Lin
- College of Food Science and Technology, Hainan University, Haikou, 570228, People's Republic of China.,Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Cui-Ying Zhang
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Lu Meng
- College of Food Science and Technology, Hainan University, Haikou, 570228, People's Republic of China
| | - Xiao-Wen Bai
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Dong-Guang Xiao
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
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22
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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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23
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Maqani N, Fine RD, Shahid M, Li M, Enriquez-Hesles E, Smith JS. Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK. MICROBIAL CELL 2018; 5:233-248. [PMID: 29796388 PMCID: PMC5961917 DOI: 10.15698/mic2018.05.630] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronologically aging yeast cells are prone to adaptive regrowth, whereby mutants with a survival advantage spontaneously appear and re-enter the cell cycle in stationary phase cultures. Adaptive regrowth is especially noticeable with short-lived strains, including those defective for SNF1, the homolog of mammalian AMP-activated protein kinase (AMPK). SNF1 becomes active in response to multiple environmental stresses that occur in chronologically aging cells, including glucose depletion and oxidative stress. SNF1 is also required for the extension of chronological lifespan (CLS) by caloric restriction (CR) as defined as limiting glucose at the time of culture inoculation. To identify specific downstream SNF1 targets responsible for CLS extension during CR, we screened for adaptive regrowth mutants that restore chronological longevity to a short-lived snf1∆ parental strain. Whole genome sequencing of the adapted mutants revealed missense mutations in TPR motifs 9 and 10 of the transcriptional co-repressor Cyc8 that specifically mediate repression through the transcriptional repressor Mig1. Another mutation occurred in MIG1 itself, thus implicating the activation of Mig1-repressed genes as a key function of SNF1 in maintaining CLS. Consistent with this conclusion, the cyc8 TPR mutations partially restored growth on alternative carbon sources and significantly extended CLS compared to the snf1∆ parent. Furthermore, cyc8 TPR mutations reactivated multiple Mig1-repressed genes, including the transcription factor gene CAT8, which is responsible for activating genes of the glyoxylate and gluconeogenesis pathways. Deleting CAT8 completely blocked CLS extension by the cyc8 TPR mutations on CLS, identifying these pathways as key Snf1-regulated CLS determinants.
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Affiliation(s)
- Nazif Maqani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Ryan D Fine
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Mehreen Shahid
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Mingguang Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908.,Department of Laboratory Medicine, Jilin Medical University, Jilin, 132013, China
| | - Elisa Enriquez-Hesles
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Jeffrey S Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
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24
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Lane S, Xu H, Oh EJ, Kim H, Lesmana A, Jeong D, Zhang G, Tsai CS, Jin YS, Kim SR. Glucose repression can be alleviated by reducing glucose phosphorylation rate in Saccharomyces cerevisiae. Sci Rep 2018; 8:2613. [PMID: 29422502 PMCID: PMC5805702 DOI: 10.1038/s41598-018-20804-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/19/2018] [Indexed: 01/06/2023] Open
Abstract
Microorganisms commonly exhibit preferential glucose consumption and diauxic growth when cultured in mixtures of glucose and other sugars. Although various genetic perturbations have alleviated the effects of glucose repression on consumption of specific sugars, a broadly applicable mechanism remains unknown. Here, we report that a reduction in the rate of glucose phosphorylation alleviates the effects of glucose repression in Saccharomyces cerevisiae. Through adaptive evolution under a mixture of xylose and the glucose analog 2-deoxyglucose, we isolated a mutant strain capable of simultaneously consuming glucose and xylose. Genome sequencing of the evolved mutant followed by CRISPR/Cas9-based reverse engineering revealed that mutations in the glucose phosphorylating enzymes (Hxk1, Hxk2, Glk1) were sufficient to confer simultaneous glucose and xylose utilization. We then found that varying hexokinase expression with an inducible promoter led to the simultaneous utilization of glucose and xylose. Interestingly, no mutations in sugar transporters occurred during the evolution, and no specific transporter played an indispensable role in simultaneous sugar utilization. Additionally, we demonstrated that slowing glucose consumption also enabled simultaneous utilization of glucose and galactose. These results suggest that the rate of intracellular glucose phosphorylation is a decisive factor for metabolic regulations of mixed sugars.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Haiqing Xu
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Eun Joong Oh
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anastashia Lesmana
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Guochang Zhang
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ching-Sung Tsai
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. .,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea. .,Institute of Agricultural Science & Technology, Kyungpook National University, Daegu, Republic of Korea.
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25
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Adnan M, Zheng W, Islam W, Arif M, Abubakar YS, Wang Z, Lu G. Carbon Catabolite Repression in Filamentous Fungi. Int J Mol Sci 2017; 19:ijms19010048. [PMID: 29295552 PMCID: PMC5795998 DOI: 10.3390/ijms19010048] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022] Open
Abstract
Carbon Catabolite Repression (CCR) has fascinated scientists and researchers around the globe for the past few decades. This important mechanism allows preferential utilization of an energy-efficient and readily available carbon source over relatively less easily accessible carbon sources. This mechanism helps microorganisms to obtain maximum amount of glucose in order to keep pace with their metabolism. Microorganisms assimilate glucose and highly favorable sugars before switching to less-favored sources of carbon such as organic acids and alcohols. In CCR of filamentous fungi, CreA acts as a transcription factor, which is regulated to some extent by ubiquitination. CreD-HulA ubiquitination ligase complex helps in CreA ubiquitination, while CreB-CreC deubiquitination (DUB) complex removes ubiquitin from CreA, which causes its activation. CCR of fungi also involves some very crucial elements such as Hexokinases, cAMP, Protein Kinase (PKA), Ras proteins, G protein-coupled receptor (GPCR), Adenylate cyclase, RcoA and SnfA. Thorough study of molecular mechanism of CCR is important for understanding growth, conidiation, virulence and survival of filamentous fungi. This review is a comprehensive revision of the regulation of CCR in filamentous fungi as well as an updated summary of key regulators, regulation of different CCR-dependent mechanisms and its impact on various physical characteristics of filamentous fungi.
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Affiliation(s)
- Muhammad Adnan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Waqar Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Arif
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yakubu Saddeeq Abubakar
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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26
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Rajvanshi PK, Arya M, Rajasekharan R. The stress-regulatory transcription factors Msn2 and Msn4 regulate fatty acid oxidation in budding yeast. J Biol Chem 2017; 292:18628-18643. [PMID: 28924051 DOI: 10.1074/jbc.m117.801704] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/12/2017] [Indexed: 11/06/2022] Open
Abstract
The transcription factors Msn2 and Msn4 (multicopy suppressor of SNF1 mutation proteins 2 and 4) bind the stress-response element in gene promoters in the yeast Saccharomyces cerevisiae However, the roles of Msn2/4 in primary metabolic pathways such as fatty acid β-oxidation are unclear. Here, in silico analysis revealed that the promoters of most genes involved in the biogenesis, function, and regulation of the peroxisome contain Msn2/4-binding sites. We also found that transcript levels of MSN2/MSN4 are increased in glucose-depletion conditions and that during growth in nonpreferred carbon sources, Msn2 is constantly localized to the nucleus in wild-type cells. Of note, the double mutant msn2Δmsn4Δ exhibited a severe growth defect when grown with oleic acid as the sole carbon source and had reduced transcript levels of major β-oxidation genes. ChIP indicated that Msn2 has increased occupancy on the promoters of β-oxidation genes in glucose-depleted conditions, and in vivo reporter gene analysis indicated reduced expression of these genes in msn2Δmsn4Δ cells. Moreover, mobility shift assays revealed that Msn4 binds β-oxidation gene promoters. Immunofluorescence microscopy with anti-peroxisome membrane protein antibodies disclosed that the msn2Δmsn4Δ strain had fewer peroxisomes than the wild type, and lipid analysis indicated that the msn2Δmsn4Δ strain had increased triacylglycerol and steryl ester levels. Collectively, our data suggest that Msn2/Msn4 transcription factors activate expression of the genes involved in fatty acid oxidation. Because glucose sensing, signaling, and fatty acid β-oxidation pathways are evolutionarily conserved throughout eukaryotes, the msn2Δmsn4Δ strain could therefore be a good model system for further study of these critical processes.
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Affiliation(s)
- Praveen Kumar Rajvanshi
- From the Department of Lipid Science of the Lipidomic Centre and.,the Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India
| | - Madhuri Arya
- From the Department of Lipid Science of the Lipidomic Centre and.,the Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India
| | - Ram Rajasekharan
- From the Department of Lipid Science of the Lipidomic Centre and .,the Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India
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27
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Epigenetic Transcriptional Memory of GAL Genes Depends on Growth in Glucose and the Tup1 Transcription Factor in Saccharomyces cerevisiae. Genetics 2017; 206:1895-1907. [PMID: 28607146 DOI: 10.1534/genetics.117.201632] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/09/2017] [Indexed: 01/01/2023] Open
Abstract
Previously expressed inducible genes can remain poised for faster reactivation for multiple cell divisions, a conserved phenomenon called epigenetic transcriptional memory. The GAL genes in Saccharomyces cerevisiae show faster reactivation for up to seven generations after being repressed. During memory, previously produced Gal1 protein enhances the rate of reactivation of GAL1, GAL10, GAL2, and GAL7 These genes also interact with the nuclear pore complex (NPC) and localize to the nuclear periphery both when active and during memory. Peripheral localization of GAL1 during memory requires the Gal1 protein, a memory-specific cis-acting element in the promoter, and the NPC protein Nup100 However, unlike other examples of transcriptional memory, the interaction with NPC is not required for faster GAL gene reactivation. Rather, downstream of Gal1, the Tup1 transcription factor and growth in glucose promote GAL transcriptional memory. Cells only show signs of memory and only benefit from memory when growing in glucose. Tup1 promotes memory-specific chromatin changes at the GAL1 promoter: incorporation of histone variant H2A.Z and dimethylation of histone H3, lysine 4. Tup1 and H2A.Z function downstream of Gal1 to promote binding of a preinitiation form of RNA Polymerase II at the GAL1 promoter, poising the gene for faster reactivation. This mechanism allows cells to integrate a previous experience (growth in galactose, reflected by Gal1 levels) with current conditions (growth in glucose, potentially through Tup1 function) to overcome repression and to poise critical GAL genes for future reactivation.
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28
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Abstract
The survival of all organisms is dependent on complex, coordinated responses to environmental cues. Non-coding RNAs have been identified as major players in regulation of gene expression, with recent evidence supporting roles for long non-coding (lnc)RNAs in both transcriptional and post-transcriptional control. Evidence from our laboratory shows that lncRNAs have the ability to form hybridized structures called R-loops with specific DNA target sequences in S. cerevisiae, thereby modulating gene expression. In this Point of View, we provide an overview of the nature of lncRNA-mediated control of gene expression in the context of our studies using the GAL gene cluster as a model for controlling the timing of transcription.
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Affiliation(s)
- Zachary T Beck
- a Department of Biochemistry , Purdue University , West Lafayette , IN , USA
| | - Zheng Xing
- a Department of Biochemistry , Purdue University , West Lafayette , IN , USA
| | - Elizabeth J Tran
- a Department of Biochemistry , Purdue University , West Lafayette , IN , USA.,b Purdue University Center for Cancer Research, Purdue University , West Lafayette , IN , USA
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29
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Dugan A, Majmudar CY, Pricer R, Niessen S, Lancia JK, Fung HYH, Cravatt BF, Mapp AK. Discovery of Enzymatic Targets of Transcriptional Activators via in Vivo Covalent Chemical Capture. J Am Chem Soc 2016; 138:12629-35. [PMID: 27611834 PMCID: PMC5217703 DOI: 10.1021/jacs.6b07680] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The network of activator protein-protein interactions (PPIs) that underpin transcription initiation is poorly defined, particularly in the cellular context. The transient nature of these contacts and the often low abundance of the participants present significant experimental hurdles. Through the coupling of in vivo covalent chemical capture and shotgun LC-MS/MS (MuDPIT) analysis, we can trap the PPIs of transcriptional activators in a cellular setting and identify the binding partners in an unbiased fashion. Using this approach, we discover that the prototypical activators Gal4 and VP16 target the Snf1 (AMPK) kinase complex via direct interactions with both the core enzymatic subunit Snf1 and the exchangeable subunit Gal83. Further, we use a tandem reversible formaldehyde and irreversible covalent chemical capture approach (TRIC) to capture the Gal4-Snf1 interaction at the Gal1 promoter in live yeast. Together, these data support a critical role for activator PPIs in both the recruitment and positioning of important enzymatic complexes at a gene promoter and represent a technical advancement in the discovery of new cellular binding targets of transcriptional activators.
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Affiliation(s)
- Amanda Dugan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chinmay Y. Majmudar
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel Pricer
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sherry Niessen
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jody K. Lancia
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hugo Yik-Hong Fung
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Anna K. Mapp
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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30
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Cloutier SC, Wang S, Ma WK, Al Husini N, Dhoondia Z, Ansari A, Pascuzzi PE, Tran EJ. Regulated Formation of lncRNA-DNA Hybrids Enables Faster Transcriptional Induction and Environmental Adaptation. Mol Cell 2016; 61:393-404. [PMID: 26833086 DOI: 10.1016/j.molcel.2015.12.024] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/23/2015] [Accepted: 12/18/2015] [Indexed: 10/22/2022]
Abstract
Long non-coding (lnc)RNAs, once thought to merely represent noise from imprecise transcription initiation, have now emerged as major regulatory entities in all eukaryotes. In contrast to the rapidly expanding identification of individual lncRNAs, mechanistic characterization has lagged behind. Here we provide evidence that the GAL lncRNAs in the budding yeast S. cerevisiae promote transcriptional induction in trans by formation of lncRNA-DNA hybrids or R-loops. The evolutionarily conserved RNA helicase Dbp2 regulates formation of these R-loops as genomic deletion or nuclear depletion results in accumulation of these structures across the GAL cluster gene promoters and coding regions. Enhanced transcriptional induction is manifested by lncRNA-dependent displacement of the Cyc8 co-repressor and subsequent gene looping, suggesting that these lncRNAs promote induction by altering chromatin architecture. Moreover, the GAL lncRNAs confer a competitive fitness advantage to yeast cells because expression of these non-coding molecules correlates with faster adaptation in response to an environmental switch.
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Affiliation(s)
- Sara C Cloutier
- Department of Biochemistry, Purdue University, BCHM 305, 175 S. University Street, West Lafayette, IN 47907, USA
| | - Siwen Wang
- Department of Biochemistry, Purdue University, BCHM 305, 175 S. University Street, West Lafayette, IN 47907, USA
| | - Wai Kit Ma
- Department of Biochemistry, Purdue University, BCHM 305, 175 S. University Street, West Lafayette, IN 47907, USA
| | - Nadra Al Husini
- Department of Biological Sciences, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, USA
| | - Zuzer Dhoondia
- Department of Biological Sciences, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, USA
| | - Athar Ansari
- Department of Biological Sciences, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, USA
| | - Pete E Pascuzzi
- Department of Biochemistry, Purdue University, BCHM 305, 175 S. University Street, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN 47907, USA; Purdue University Libraries, 504 W. State Street, West Lafayette, IN 47907, USA.
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, BCHM 305, 175 S. University Street, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN 47907, USA.
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31
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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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32
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Zhang CY, Bai XW, Lin X, Liu XE, Xiao DG. Effects of SNF1 on Maltose Metabolism and Leavening Ability of Baker's Yeast in Lean Dough. J Food Sci 2015; 80:M2879-85. [PMID: 26580148 DOI: 10.1111/1750-3841.13137] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/05/2015] [Indexed: 11/29/2022]
Abstract
Maltose metabolism of baker's yeast (Saccharomyces cerevisiae) in lean dough is negatively influenced by glucose repression, thereby delaying the dough fermentation. To improve maltose metabolism and leavening ability, it is necessary to alleviate glucose repression. The Snf1 protein kinase is well known to be essential for the response to glucose repression and required for transcription of glucose-repressed genes including the maltose-utilization genes (MAL). In this study, the SNF1 overexpression and deletion industrial baker's yeast strains were constructed and characterized in terms of maltose utilization, growth and fermentation characteristics, mRNA levels of MAL genes (MAL62 encoding the maltase and MAL61 encoding the maltose permease) and maltase and maltose permease activities. Our results suggest that overexpression of SNF1 was effective to glucose derepression for enhancing MAL expression levels and enzymes (maltase and maltose permease) activities. These enhancements could result in an 18% increase in maltose metabolism of industrial baker's yeast in LSMLD medium (the low sugar model liquid dough fermentation medium) containing glucose and maltose and a 15% increase in leavening ability in lean dough. These findings provide a valuable insight of breeding industrial baker's yeast for rapid fermentation.
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Affiliation(s)
- Cui-Ying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin Univ. of Science and Technology, Tianjin, 300457, P. R. China
| | - Xiao-Wen Bai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin Univ. of Science and Technology, Tianjin, 300457, P. R. China
| | - Xue Lin
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin Univ. of Science and Technology, Tianjin, 300457, P. R. China
| | - Xiao-Er Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin Univ. of Science and Technology, Tianjin, 300457, P. R. China
| | - Dong-Guang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin Univ. of Science and Technology, Tianjin, 300457, P. R. China
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33
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Nguyen-Huu TD, Gupta C, Ma B, Ott W, Josić K, Bennett MR. Timing and Variability of Galactose Metabolic Gene Activation Depend on the Rate of Environmental Change. PLoS Comput Biol 2015. [PMID: 26200924 PMCID: PMC4511807 DOI: 10.1371/journal.pcbi.1004399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Modulation of gene network activity allows cells to respond to changes in environmental conditions. For example, the galactose utilization network in Saccharomyces cerevisiae is activated by the presence of galactose but repressed by glucose. If both sugars are present, the yeast will first metabolize glucose, depleting it from the extracellular environment. Upon depletion of glucose, the genes encoding galactose metabolic proteins will activate. Here, we show that the rate at which glucose levels are depleted determines the timing and variability of galactose gene activation. Paradoxically, we find that Gal1p, an enzyme needed for galactose metabolism, accumulates more quickly if glucose is depleted slowly rather than taken away quickly. Furthermore, the variability of induction times in individual cells depends non-monotonically on the rate of glucose depletion and exhibits a minimum at intermediate depletion rates. Our mathematical modeling suggests that the dynamics of the metabolic transition from glucose to galactose are responsible for the variability in galactose gene activation. These findings demonstrate that environmental dynamics can determine the phenotypic outcome at both the single-cell and population levels. Understanding how cells respond to environmental changes is a fundamental question in biology. Such responses are governed by interactions between genes, proteins and other cellular machinery. However, even the responses of genetically identical cells are not identical. Our aim was to examine the origins of this variability using the galactose metabolic network in the baker yeast Saccharomyces cerevisiae. This metabolic network allows yeast to consume galactose once its preferred carbon source, glucose, is depleted. We used microfluidic devices and time-lapse fluorescence microscopy to observe how individual cells respond as glucose is removed from their environment at different rates. We found that the activation of the galactose metabolic network depends on the rate of depletion. Surprisingly, cells start to consume galactose faster when glucose is depleted slowly rather than removed quickly. Furthermore, genetically identical cells can exhibit remarkably different rates of galactose consumption. We provide a simple mathematical model that explains these different observations. These results suggest that dynamic changes of environmental conditions can affect the behavior of both individual cells and the whole population.
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Affiliation(s)
- Truong D. Nguyen-Huu
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Chinmaya Gupta
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
| | - Bo Ma
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - William Ott
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Matthew R. Bennett
- Department of Biosciences, Rice University, Houston, Texas, United States of America
- Institute of Biosciences and Bioengineering, Rice University, Houston, Texas, United States of America
- * E-mail:
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34
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Chantranupong L, Wolfson RL, Sabatini DM. Nutrient-sensing mechanisms across evolution. Cell 2015; 161:67-83. [PMID: 25815986 DOI: 10.1016/j.cell.2015.02.041] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Indexed: 12/11/2022]
Abstract
For organisms to coordinate their growth and development with nutrient availability, they must be able to sense nutrient levels in their environment. Here, we review select nutrient-sensing mechanisms in a few diverse organisms. We discuss how these mechanisms reflect the nutrient requirements of specific species and how they have adapted to the emergence of multicellularity in eukaryotes.
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Affiliation(s)
- Lynne Chantranupong
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rachel L Wolfson
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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35
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Schuler D, Wahl R, Wippel K, Vranes M, Münsterkötter M, Sauer N, Kämper J. Hxt1, a monosaccharide transporter and sensor required for virulence of the maize pathogen Ustilago maydis. THE NEW PHYTOLOGIST 2015; 206:1086-1100. [PMID: 25678342 DOI: 10.1111/nph.13314] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/23/2014] [Indexed: 05/23/2023]
Abstract
The smut Ustilago maydis, a ubiquitous pest of corn, is highly adapted to its host to parasitize on its organic carbon sources. We have identified a hexose transporter, Hxt1, as important for fungal development during both the saprophytic and the pathogenic stage of the fungus. Hxt1 was characterized as a high-affinity transporter for glucose, fructose, and mannose; ∆hxt1 strains show significantly reduced growth on these substrates, setting Hxt1 as the main hexose transporter during saprophytic growth. After plant infection, ∆hxt1 strains show decreased symptom development. However, expression of a Hxt1 protein with a mutation leading to constitutively active signaling in the yeast glucose sensors Snf3p and Rgt2p results in completely apathogenic strains. Fungal development is stalled immediately after plant penetration, implying a dual function of Hxt1 as transporter and sensor. As glucose sensors are only known for yeasts, 'transceptor' as Hxt1 may constitute a general mechanism for sensing of glucose in fungi. In U. maydis, Hxt1 links a nutrient-dependent environmental signal to the developmental program during pathogenic development.
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Affiliation(s)
- David Schuler
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology, Hertzstrasse 16, Karlsruhe, 76187, Germany
| | - Ramon Wahl
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology, Hertzstrasse 16, Karlsruhe, 76187, Germany
| | - Kathrin Wippel
- Molecular Plant Physiology, Friedrich Alexander University Erlangen-Nuremberg, Staudtstrasse 5, Erlangen, 91058, Germany
| | - Miroslav Vranes
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology, Hertzstrasse 16, Karlsruhe, 76187, Germany
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Norbert Sauer
- Molecular Plant Physiology, Friedrich Alexander University Erlangen-Nuremberg, Staudtstrasse 5, Erlangen, 91058, Germany
| | - Jörg Kämper
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology, Hertzstrasse 16, Karlsruhe, 76187, Germany
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36
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Affiliation(s)
- Jan Schirawski
- Microbial Genetics, Institute for Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
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37
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Almquist J, Bendrioua L, Adiels CB, Goksör M, Hohmann S, Jirstrand M. A Nonlinear Mixed Effects Approach for Modeling the Cell-To-Cell Variability of Mig1 Dynamics in Yeast. PLoS One 2015; 10:e0124050. [PMID: 25893847 PMCID: PMC4404321 DOI: 10.1371/journal.pone.0124050] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/25/2015] [Indexed: 11/29/2022] Open
Abstract
The last decade has seen a rapid development of experimental techniques that allow data collection from individual cells. These techniques have enabled the discovery and characterization of variability within a population of genetically identical cells. Nonlinear mixed effects (NLME) modeling is an established framework for studying variability between individuals in a population, frequently used in pharmacokinetics and pharmacodynamics, but its potential for studies of cell-to-cell variability in molecular cell biology is yet to be exploited. Here we take advantage of this novel application of NLME modeling to study cell-to-cell variability in the dynamic behavior of the yeast transcription repressor Mig1. In particular, we investigate a recently discovered phenomenon where Mig1 during a short and transient period exits the nucleus when cells experience a shift from high to intermediate levels of extracellular glucose. A phenomenological model based on ordinary differential equations describing the transient dynamics of nuclear Mig1 is introduced, and according to the NLME methodology the parameters of this model are in turn modeled by a multivariate probability distribution. Using time-lapse microscopy data from nearly 200 cells, we estimate this parameter distribution according to the approach of maximizing the population likelihood. Based on the estimated distribution, parameter values for individual cells are furthermore characterized and the resulting Mig1 dynamics are compared to the single cell times-series data. The proposed NLME framework is also compared to the intuitive but limited standard two-stage (STS) approach. We demonstrate that the latter may overestimate variabilities by up to almost five fold. Finally, Monte Carlo simulations of the inferred population model are used to predict the distribution of key characteristics of the Mig1 transient response. We find that with decreasing levels of post-shift glucose, the transient response of Mig1 tend to be faster, more extended, and displays an increased cell-to-cell variability.
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Affiliation(s)
- Joachim Almquist
- Fraunhofer-Chalmers Centre, Chalmers Science Park, Göteborg, Sweden
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- * E-mail:
| | - Loubna Bendrioua
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
- Department of Physics, University of Gothenburg, Göteborg, Sweden
| | | | - Mattias Goksör
- Department of Physics, University of Gothenburg, Göteborg, Sweden
| | - Stefan Hohmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Mats Jirstrand
- Fraunhofer-Chalmers Centre, Chalmers Science Park, Göteborg, Sweden
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Sumoylation and transcription regulation at nuclear pores. Chromosoma 2014; 124:45-56. [PMID: 25171917 PMCID: PMC4339684 DOI: 10.1007/s00412-014-0481-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 01/22/2023]
Abstract
Increasing evidence indicates that besides promoters, enhancers, and epigenetic modifications, nuclear organization is another parameter contributing to optimal control of gene expression. Although differences between species exist, the influence of gene positioning on expression seems to be a conserved feature from yeast to Drosophila and mammals. The nuclear periphery is one of the nuclear compartments implicated in gene regulation. It consists of the nuclear envelope (NE) and the nuclear pore complexes (NPC), which have distinct roles in the control of gene expression. The NPC has recently been shown to tether proteins involved in the sumoylation pathway. Here, we will focus on the importance of gene positioning and NPC-linked sumoylation/desumoylation in transcription regulation. We will mainly discuss observations made in the yeast Saccharomyces cerevisiae model system and highlight potential parallels in metazoan species.
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Lin X, Zhang CY, Bai XW, Song HY, Xiao DG. Effects of MIG1, TUP1 and SSN6 deletion on maltose metabolism and leavening ability of baker's yeast in lean dough. Microb Cell Fact 2014; 13:93. [PMID: 24993311 PMCID: PMC4094228 DOI: 10.1186/s12934-014-0093-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 06/18/2014] [Indexed: 11/17/2022] Open
Abstract
Background Glucose repression is a global regulatory system in baker’s yeast. Maltose metabolism in baker’s yeast strains is negatively influenced by glucose, thereby affecting metabolite productivity (leavening ability in lean dough). Even if the general repression system constituted by MIG1, TUP1 and SSN6 factors has already been reported, the functions of these three genes in maltose metabolism remain unclear. In this work, we explored the effects of MIG1 and/or TUP1 and/or SSN6 deletion on the alleviation of glucose-repression to promote maltose metabolism and leavening ability of baker’s yeast. Results Results strongly suggest that the deletion of MIG1 and/or TUP1 and/or SSN6 can exert various effects on glucose repression for maltose metabolism. The deletion of TUP1 was negative for glucose derepression to facilitate the maltose metabolism. By contrast, the deletion of MIG1 and/or SSN6, rather than other double-gene or triple-gene mutations could partly relieve glucose repression, thereby promoting maltose metabolism and the leavening ability of baker’s yeast in lean dough. Conclusions The mutants of industrial baker’s yeast with enhanced maltose metabolism and leavening ability in lean dough were developed by genetic engineering. These baker’s yeast strains had excellent potential industrial applications.
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Affiliation(s)
| | - Cui-Ying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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40
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Ye T, Bendrioua L, Carmena D, García-Salcedo R, Dahl P, Carling D, Hohmann S. The mammalian AMP-activated protein kinase complex mediates glucose regulation of gene expression in the yeast Saccharomyces cerevisiae. FEBS Lett 2014; 588:2070-7. [PMID: 24815694 DOI: 10.1016/j.febslet.2014.04.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 04/21/2014] [Accepted: 04/24/2014] [Indexed: 11/24/2022]
Abstract
The AMP-activated protein kinase (AMPK) controls energy homeostasis in eukaryotic cells. Here we expressed hetero-trimeric mammalian AMPK complexes in a Saccharomyces cerevisiae mutant lacking all five genes encoding yeast AMPK/SNF1 components. Certain mammalian complexes complemented the growth defect of the yeast mutant on non-fermentable carbon sources. Phosphorylation of the AMPK α1-subunit was glucose-regulated, albeit not by the Glc7-Reg1/2 phosphatase, which performs this function on yeast AMPK/SNF1. AMPK could take over SNF1 function in glucose derepression. While indirectly acting anti-diabetic drugs had no effect on AMPK in yeast, compound 991 stimulated α1-subunit phosphorylation. Our results demonstrate a remarkable functional conservation of AMPK and that glucose regulation of AMPK may not be mediated by regulatory features of a specific phosphatase.
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Affiliation(s)
- Tian Ye
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Göteborg, Sweden
| | - Loubna Bendrioua
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Göteborg, Sweden
| | - David Carmena
- MRC Clinical Sciences Centre, Cellular Stress Group, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Raúl García-Salcedo
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Göteborg, Sweden
| | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Göteborg, Sweden
| | - David Carling
- MRC Clinical Sciences Centre, Cellular Stress Group, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Stefan Hohmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Göteborg, Sweden.
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41
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Rødkaer SV, Faergeman NJ. Glucose- and nitrogen sensing and regulatory mechanisms inSaccharomyces cerevisiae. FEMS Yeast Res 2014; 14:683-96. [DOI: 10.1111/1567-1364.12157] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/11/2014] [Accepted: 04/13/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Steven V. Rødkaer
- Villum Center for Bioanalytical Sciences; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense M Denmark
| | - Nils J. Faergeman
- Villum Center for Bioanalytical Sciences; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense M Denmark
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42
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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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43
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García-Salcedo R, Lubitz T, Beltran G, Elbing K, Tian Y, Frey S, Wolkenhauer O, Krantz M, Klipp E, Hohmann S. Glucose de-repression by yeast AMP-activated protein kinase SNF1 is controlled via at least two independent steps. FEBS J 2014; 281:1901-17. [PMID: 24529170 DOI: 10.1111/febs.12753] [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] [Received: 12/15/2013] [Revised: 02/03/2014] [Accepted: 02/10/2014] [Indexed: 12/14/2022]
Abstract
The AMP-activated protein kinase, AMPK, controls energy homeostasis in eukaryotic cells but little is known about the mechanisms governing the dynamics of its activation/deactivation. The yeast AMPK, SNF1, is activated in response to glucose depletion and mediates glucose de-repression by inactivating the transcriptional repressor Mig1. Here we show that overexpression of the Snf1-activating kinase Sak1 results, in the presence of glucose, in constitutive Snf1 activation without alleviating glucose repression. Co-overexpression of the regulatory subunit Reg1 of the Glc-Reg1 phosphatase complex partly restores glucose regulation of Snf1. We generated a set of 24 kinetic mathematical models based on dynamic data of Snf1 pathway activation and deactivation. The models that reproduced our experimental observations best featured (a) glucose regulation of both Snf1 phosphorylation and dephosphorylation, (b) determination of the Mig1 phosphorylation status in the absence of glucose by Snf1 activity only and (c) a regulatory step directing active Snf1 to Mig1 under glucose limitation. Hence it appears that glucose de-repression via Snf1-Mig1 is regulated by glucose via at least two independent steps: the control of activation of the Snf1 kinase and directing active Snf1 to inactivating its target Mig1.
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Affiliation(s)
- Raúl García-Salcedo
- Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden
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44
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Wang S, Tran EJ. Unexpected functions of lncRNAs in gene regulation. Commun Integr Biol 2014; 6:e27610. [PMID: 24563719 DOI: 10.4161/cib.27610] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a group of molecules that function in gene regulation in yeast, plants and mammals. The precise mechanisms of action for lncRNAs, however, remain largely unclear. The GAL gene cluster has been used as a model system to study the function of these molecules in Saccharomyces cerevisiae, with a historical focus on lncRNA-dependent repression. Strikingly, in characterizing the role of the RNA helicase Dbp2, we discovered that the GAL lncRNAs could also promote transcriptional activation of the targeted GAL protein-coding genes. Interestingly, these lncRNAs help determine how quickly the GAL genes can be induced in response to galactose, without altering final steady-state transcript levels. This unexpected finding suggests that one role for lncRNAs is to promote the timing of gene expression. Herein, we discuss our discoveries in the context of current models of lncRNA functions in eukaryotes, with a key emphasis on future challenges for genomic research.
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Affiliation(s)
- Siwen Wang
- Department of Biochemistry; Purdue University; West Lafayette, IN USA
| | - Elizabeth J Tran
- Department of Biochemistry; Purdue University; West Lafayette, IN USA ; Purdue University Center for Cancer Research; Purdue University; West Lafayette, IN USA
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45
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Roy A, Jouandot D, Cho KH, Kim JH. Understanding the mechanism of glucose-induced relief of Rgt1-mediated repression in yeast. FEBS Open Bio 2014; 4:105-11. [PMID: 24490134 PMCID: PMC3907687 DOI: 10.1016/j.fob.2013.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/05/2013] [Accepted: 12/24/2013] [Indexed: 11/24/2022] Open
Abstract
The yeast Rgt1 repressor inhibits transcription of the glucose transporter (HXT) genes in the absence of glucose. It does so by recruiting the general corepressor complex Ssn6-Tup1 and the HXT corepressor Mth1. In the presence of glucose, Rgt1 is phosphorylated by the cAMP-activated protein kinase A (PKA) and dissociates from the HXT promoters, resulting in expression of HXT genes. In this study, using Rgt1 chimeras that bind DNA constitutively, we investigate how glucose regulates Rgt1 function. Our results show that the DNA-bound Rgt1 constructs repress expression of the HXT1 gene in conjunction with Ssn6-Tup1 and Mth1, and that this repression is lifted when they dissociate from Ssn6-Tup1 in high glucose conditions. Mth1 mediates the interaction between the Rgt1 constructs and Ssn6-Tup1, and glucose-induced downregulation of Mth1 enables PKA to phosphorylate the Rgt1 constructs. This phosphorylation induces dissociation of Ssn6-Tup1 from the DNA-bound Rgt1 constructs, resulting in derepression of HXT gene expression. Therefore, Rgt1 removal from DNA occurs in response to glucose but is not necessary for glucose induction of HXT gene expression, suggesting that glucose regulates Rgt1 function by primarily modulating the Rgt1 interaction with Ssn6-Tup1. Rgt1 represses gene expression by recruiting Ssn6-Tup1 to its target promoters. Dissociation of Rgt1 from DNA is not required to lift Rgt1-mediated repression. Rgt1 dissociation from Ssn6-Tup1 is sufficient for derepression of its target genes.
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Affiliation(s)
- Adhiraj Roy
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical Center, 2300 Eye Street, Washington, DC 20037, USA
| | - David Jouandot
- Department of Biological Sciences, The University of Southern Mississippi, 118 College Dr., Hattiesburg, MS 39406, USA
| | - Kyu Hong Cho
- Department of Microbiology, Southern Illinois University Carbondale, 1125 Lincoln Drive, Carbondale, IL 62901, USA
| | - Jeong-Ho Kim
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical Center, 2300 Eye Street, Washington, DC 20037, USA
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Texari L, Dieppois G, Vinciguerra P, Contreras MP, Groner A, Letourneau A, Stutz F. The nuclear pore regulates GAL1 gene transcription by controlling the localization of the SUMO protease Ulp1. Mol Cell 2013; 51:807-18. [PMID: 24074957 DOI: 10.1016/j.molcel.2013.08.047] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 07/17/2013] [Accepted: 08/20/2013] [Indexed: 12/15/2022]
Abstract
Transcription activation of some yeast genes correlates with their repositioning to the nuclear pore complex (NPC). The NPC-bound Mlp1 and Mlp2 proteins have been shown to associate with the GAL1 gene promoter and to maintain Ulp1, a key SUMO protease, at the NPC. Here, we show that the release of Ulp1 from the NPC increases the kinetics of GAL1 derepression, whereas artificial NPC anchoring of Ulp1 in the Δmlp1/2 strain restores normal GAL1 regulation. Moreover, artificial tethering of the Ulp1 catalytic domain to the GAL1 locus enhances the derepression kinetics. Our results also indicate that Ulp1 modulates the sumoylation state of Tup1 and Ssn6, two regulators of glucose-repressed genes, and that a loss of Ssn6 sumoylation correlates with an increase in GAL1 derepression kinetics. Altogether, our data highlight a role for the NPC-associated SUMO protease Ulp1 in regulating the sumoylation of gene-bound transcription regulators, positively affecting transcription kinetics in the context of the NPC.
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Affiliation(s)
- Lorane Texari
- Department of Cell Biology, NCCR Frontiers in Genetics, iGE3, University of Geneva, Geneva 1211, Switzerland
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47
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Cloutier SC, Wang S, Ma WK, Petell CJ, Tran EJ. Long noncoding RNAs promote transcriptional poising of inducible genes. PLoS Biol 2013; 11:e1001715. [PMID: 24260025 PMCID: PMC3833879 DOI: 10.1371/journal.pbio.1001715] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/09/2013] [Indexed: 11/19/2022] Open
Abstract
The GAL cluster-associated long non-coding RNAs (lncRNAs) promote rapid induction of GAL genes in budding yeast, thereby promoting a faster switch in transcriptional programs when needed. Long noncoding RNAs (lncRNAs) are a class of molecules that impinge on the expression of protein-coding genes. Previous studies have suggested that the GAL cluster-associated lncRNAs of Saccharomyces cerevisiae repress expression of the protein-coding GAL genes. Herein, we demonstrate a previously unrecognized role for the GAL lncRNAs in activating gene expression. In yeast strains lacking the RNA helicase, DBP2, or the RNA decay enzyme, XRN1, we find that the GAL lncRNAs specifically accelerate gene expression from a prior repressive state. Furthermore, we provide evidence that the previously suggested repressive role is a result of specific mutant phenotypes, rather than a reflection of the normal, wild-type function of these noncoding RNAs. To shed light on the mechanism for lncRNA-dependent gene activation, we show that rapid induction of the protein-coding GAL genes is associated with faster recruitment of RNA polymerase II and reduced association of transcriptional repressors with GAL gene promoters. This suggests that the GAL lncRNAs enhance expression by derepressing the GAL genes. Consistently, the GAL lncRNAs enhance the kinetics of transcriptional induction, promoting faster expression of the protein-coding GAL genes upon the switch in carbon source. We suggest that the GAL lncRNAs poise inducible genes for rapid activation, enabling cells to more effectively trigger new transcriptional programs in response to cellular cues. Long noncoding RNAs (lncRNAs) are a recently identified class of molecules that regulate the expression of protein-coding genes through a number of mechanisms, some of them poorly characterized. The GAL gene cluster of the yeast Saccharomyces cerevisiae encodes a series of three inducible genes that are turned on or off by the presence or absence of specific carbon sources in the environment. Previous studies have documented the presence of two lncRNAs—GAL10 and GAL10s—encoded by genes that overlap the GAL cluster. We have now uncovered a role for both these lncRNAs in promoting the activation of the GAL genes when they are released from repressive conditions. This activation occurs at the kinetic level, through more rapid recruitment of RNA polymerase II and decreased association of the co-repressor, Cyc8. Under normal conditions, but also especially when they are stabilized and their levels are up-regulated, these GAL lncRNAs promote faster GAL gene activation. We suggest that these lncRNA molecules poise inducible genes for quick response to extracellular cues, triggering a faster switch in transcriptional programs.
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Affiliation(s)
- Sara C. Cloutier
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Siwen Wang
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Wai Kit Ma
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Christopher J. Petell
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Elizabeth J. Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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48
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The yeast AMPK homolog SNF1 regulates acetyl coenzyme A homeostasis and histone acetylation. Mol Cell Biol 2013; 33:4701-17. [PMID: 24081331 DOI: 10.1128/mcb.00198-13] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetyl coenzyme A (acetyl-CoA) is a key metabolite at the crossroads of metabolism, signaling, chromatin structure, and transcription. Concentration of acetyl-CoA affects histone acetylation and links intermediary metabolism and transcriptional regulation. Here we show that SNF1, the budding yeast ortholog of the mammalian AMP-activated protein kinase (AMPK), plays a role in the regulation of acetyl-CoA homeostasis and global histone acetylation. SNF1 phosphorylates and inhibits acetyl-CoA carboxylase, which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the first and rate-limiting reaction in the de novo synthesis of fatty acids. Inactivation of SNF1 results in a reduced pool of cellular acetyl-CoA, globally decreased histone acetylation, and reduced fitness and stress resistance. The histone acetylation and transcriptional defects can be partially suppressed and the overall fitness improved in snf1Δ mutant cells by increasing the cellular concentration of acetyl-CoA, indicating that the regulation of acetyl-CoA homeostasis represents another mechanism in the SNF1 regulatory repertoire.
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Yang S, Guarnieri MT, Smolinski S, Ghirardi M, Pienkos PT. De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:118. [PMID: 23971877 PMCID: PMC3846465 DOI: 10.1186/1754-6834-6-118] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 08/05/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microalgae can make a significant contribution towards meeting global renewable energy needs in both carbon-based and hydrogen (H2) biofuel. The development of energy-related products from algae could be accelerated with improvements in systems biology tools, and recent advances in sequencing technology provide a platform for enhanced transcriptomic analyses. However, these techniques are still heavily reliant upon available genomic sequence data. Chlamydomonas moewusii is a unicellular green alga capable of evolving molecular H2 under both dark and light anaerobic conditions, and has high hydrogenase activity that can be rapidly induced. However, to date, there is no systematic investigation of transcriptomic profiling during induction of H2 photoproduction in this organism. RESULTS In this work, RNA-Seq was applied to investigate transcriptomic profiles during the dark anaerobic induction of H2 photoproduction. 156 million reads generated from 7 samples were then used for de novo assembly after data trimming. BlastX results against NCBI database and Blast2GO results were used to interpret the functions of the assembled 34,136 contigs, which were then used as the reference contigs for RNA-Seq analysis. Our results indicated that more contigs were differentially expressed during the period of early and higher H2 photoproduction, and fewer contigs were differentially expressed when H2-photoproduction rates decreased. In addition, C. moewusii and C. reinhardtii share core functional pathways, and transcripts for H2 photoproduction and anaerobic metabolite production were identified in both organisms. C. moewusii also possesses similar metabolic flexibility as C. reinhardtii, and the difference between C. moewusii and C. reinhardtii on hydrogenase expression and anaerobic fermentative pathways involved in redox balancing may explain their different profiles of hydrogenase activity and secreted anaerobic metabolites. CONCLUSIONS Herein, we have described a workflow using commercial software to analyze RNA-Seq data without reference genome sequence information, which can be applied to other unsequenced microorganisms. This study provided biological insights into the anaerobic fermentation and H2 photoproduction of C. moewusii, and the first transcriptomic RNA-Seq dataset of C. moewusii generated in this study also offer baseline data for further investigation (e.g. regulatory proteins related to fermentative pathway discussed in this study) of this organism as a H2-photoproduction strain.
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Affiliation(s)
| | | | - Sharon Smolinski
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Maria Ghirardi
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
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50
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Kim JH, Roy A, Jouandot D, Cho KH. The glucose signaling network in yeast. Biochim Biophys Acta Gen Subj 2013; 1830:5204-10. [PMID: 23911748 DOI: 10.1016/j.bbagen.2013.07.025] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 01/26/2023]
Abstract
BACKGROUND Most cells possess a sophisticated mechanism for sensing glucose and responding to it appropriately. Glucose sensing and signaling in the budding yeast Saccharomyces cerevisiae represent an important paradigm for understanding how extracellular signals lead to changes in the gene expression program in eukaryotes. SCOPE OF REVIEW This review focuses on the yeast glucose sensing and signaling pathways that operate in a highly regulated and cooperative manner to bring about glucose-induction of HXT gene expression. MAJOR CONCLUSIONS The yeast cells possess a family of glucose transporters (HXTs), with different kinetic properties. They employ three major glucose signaling pathways-Rgt2/Snf3, AMPK, and cAMP-PKA-to express only those transporters best suited for the amounts of glucose available. We discuss the current understanding of how these pathways are integrated into a regulatory network to ensure efficient uptake and utilization of glucose. GENERAL SIGNIFICANCE Elucidating the role of multiple glucose signals and pathways involved in glucose uptake and metabolism in yeast may reveal the molecular basis of glucose homeostasis in humans, especially under pathological conditions, such as hyperglycemia in diabetics and the elevated rate of glycolysis observed in many solid tumors.
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Affiliation(s)
- Jeong-Ho Kim
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical Center, 2300 Eye Street, Washington, DC 20037, USA.
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