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Singh V, Raheja Y, Basotra N, Sharma G, Tsang A, Chadha BS. CRISPR/Cas9 mediated gene editing of transcription factor ACE1 for enhanced cellulase production in thermophilic fungus Rasamsonia emersonii. Fungal Biol Biotechnol 2023; 10:18. [PMID: 37658430 PMCID: PMC10472679 DOI: 10.1186/s40694-023-00165-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/28/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND The filamentous fungus Rasamsonia emersonii has immense potential to produce biorefinery relevant thermostable cellulase and hemicellulase enzymes using lignocellulosic biomass. Previously in our lab, a hyper-cellulase producing strain of R. emersonii was developed through classical breeding and system biology approaches. ACE1, a pivotal transcription factor in fungi, plays a crucial role in negatively regulating the expression of cellulase genes. In order to identify the role of ACE1 in cellulase production and to further improve the lignocellulolytic enzyme production in R. emersonii, CRISPR/Cas9 mediated disruption of ACE1 gene was employed. RESULTS A gene-edited ∆ACE1 strain (GN11) was created, that showed 21.97, 20.70 and 24.63, 9.42, 18.12%, improved endoglucanase, cellobiohydrolase (CBHI), β-glucosidase, FPase, and xylanase, activities, respectively, as compared to parental strain M36. The transcriptional profiling showed that the expression of global regulator (XlnR) and different CAZymes genes including endoglucanases, cellobiohydrolase, β-xylosidase, xylanase, β-glucosidase and lytic polysaccharide mono-oxygenases (LPMOs) were significantly enhanced, suggesting critical roles of ACE1 in negatively regulating the expression of various key genes associated with cellulase production in R. emersonii. Whereas, the disruption of ACE1 significantly down-regulated the expression of CreA repressor gene as also evidenced by 2-deoxyglucose (2-DG) resistance phenotype exhibited by edited strain GN11 as well as appreciably higher constitutive production of cellulases in the presence of glucose and mixture of glucose and disaccharide (MGDs) both in batch and flask fed batch mode of culturing. Furthermore, ∆ACE1 strains were evaluated for the hydrolysis of biorefinery relevant steam/acid pretreated unwashed rice straw slurry (Praj Industries Ltd; 15% substrate loading rate) and were found to be significantly superior when compared to the benchmark enzymes produced by parent strain M36 and Cellic Ctec3. CONCLUSIONS Current work uncovers the crucial role of ACE1 in regulating the expression of the various cellulase genes and carbon catabolite repression mechanism in R. emersonii. This study represents the first successful report of utilizing CRISPR/Cas9 genome editing technology to disrupt the ACE1 gene in the thermophlic fungus R. emersonii. The improved methodologies presented in this work might be applied to other commercially important fungal strains for which genetic manipulation tools are limited.
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Affiliation(s)
- Varinder Singh
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Yashika Raheja
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Neha Basotra
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Gaurav Sharma
- Department of Microbiology, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Adrian Tsang
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC, H4B 1R6, Canada
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Identification of traits to improve co-assimilation of glucose and xylose by adaptive evolution of Spathaspora passalidarum and Scheffersomyces stipitis yeasts. Appl Microbiol Biotechnol 2023; 107:1143-1157. [PMID: 36625916 DOI: 10.1007/s00253-023-12362-1] [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: 08/26/2022] [Revised: 11/21/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023]
Abstract
Lignocellulosic biomass is a renewable raw material for producing several high-value-added chemicals and fuels. In general, xylose and glucose are the major sugars in biomass hydrolysates, and their efficient utilization by microorganisms is critical for an economical production process. Yeasts capable of co-consuming mixed sugars might lead to higher yields and productivities in industrial fermentation processes. Herein, we performed adaptive evolution assays with two xylose-fermenting yeasts, Spathaspora passalidarum and Scheffersomyces stipitis, to obtain derived clones with improved capabilities of glucose and xylose co-consumption. Adapted strains were obtained after successive growth selection using xylose and the non-metabolized glucose analog 2-deoxy-D-glucose as a selective pressure. The co-fermentation capacity of evolved and parental strains was evaluated on xylose-glucose mixtures. Our results revealed an improved co-assimilation capability by the evolved strains; however, xylose and glucose consumption were observed at slower rates than the parental yeasts. Genome resequencing of the evolved strains revealed genes affected by non-synonymous variants that might be involved with the co-consumption phenotype, including the HXT2.4 gene that encodes a putative glucose transporter in Sp. passalidarum. Expression of this mutant HXT2.4 in Saccharomyces cerevisiae improved the cells' co-assimilation of glucose and xylose. Therefore, our results demonstrated the successful improvement of co-fermentation through evolutionary engineering and the identification of potential targets for further genetic engineering of different yeast strains. KEY POINTS: • Laboratory evolution assay was used to obtain improved sugar co-consumption of non-Saccharomyces strains. • Evolved Sp. passalidarum and Sc. stipitis were able to more efficiently co-ferment glucose and xylose. • A mutant Hxt2.4 permease, which co-transports xylose and glucose, was identified.
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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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Alfatah M, Eisenhaber F. The PICLS high-throughput screening method for agents extending cellular longevity identifies 2,5-anhydro-D-mannitol as novel anti-aging compound. GeroScience 2022; 45:141-158. [PMID: 35705837 PMCID: PMC9886722 DOI: 10.1007/s11357-022-00598-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/25/2022] [Indexed: 02/03/2023] Open
Abstract
Although aging is the biggest risk factor for human chronic (cancer, diabetic, cardiovascular, and neurodegenerative) diseases, few interventions are known besides caloric restriction and a small number of drugs (with substantial side effects) that directly address aging. Thus, there is an urgent need for new options that can generally delay aging processes and prevent age-related diseases. Cellular aging is at the basis of aging processes. Chronological lifespan (CLS) of yeast Saccharomyces cerevisiae is the well-established model system for investigating the interventions of human post-mitotic cellular aging. CLS is defined as the number of days cells remain viable in a stationary phase. We developed a new, cheap, and fast quantitative method for measuring CLS in cell cultures incubated together with various chemical agents and controls on 96-well plates. Our PICLS protocol with (1) the use of propidium iodide for fluorescent-based cell survival reading in a microplate reader and (2) total cell count measurement via OD600nm absorption from the same plate provides real high-throughput capacity. Depending on logistics, large numbers of plates can be processed in parallel so that the screening of thousands of compounds becomes feasible in a short time. The method was validated by measuring the effect of rapamycin and calorie restriction on yeast CLS. We utilized this approach for chemical agent screening. We discovered the anti-aging/geroprotective potential of 2,5-anhydro-D-mannitol (2,5-AM) and suggest its usage individually or in combination with other anti-aging interventions.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Singapore, 138671, A*STAR, Singapore.
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Singapore, 138671, A*STAR, Singapore. .,Genome Institute of Singapore (GIS), Singapore, 138672, A*STAR, Singapore. .,School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, 637551, Singapore.
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Raheja Y, Singh V, Kaur B, Basotra N, Di Falco M, Tsang A, Singh Chadha B. Combination of system biology and classical approaches for developing biorefinery relevant lignocellulolytic Rasamsonia emersonii strain. BIORESOURCE TECHNOLOGY 2022; 351:127039. [PMID: 35318142 DOI: 10.1016/j.biortech.2022.127039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The objective of this study was to develop thermophilic fungus Rasamsonia emersonii using integrated system biology tools (genomics, proteomics and transcriptional analysis) in combination with classical strain breeding approaches. Developed hyper cellulolytic mutant strain M36 showed endoglucanase (476.35 U/ml), β-glucosidase (70.54 U/ml), cellobiohydrolase (15.17 U/ml), FPase (4.89 U/ml) and xylanase (485.21 U/ml) on cellulose/gram flour based production medium. Comparison of the expression profile at proteome and transcriptional level of the developed strain and wild type parent gave detailed insight into the up-regulation of different CAZymes including glycosyl hydrolases (GH5, GH6, GH7, GH3, GH10) and auxiliary enzymes (lytic polysaccharide monooxygenase, swollenin) at system level. Furthermore, the potential of lignocellulolytic enzyme produced by the developed strain and custom designed cocktail spiked with heterologously expressed lytic polysaccharide monooxygenase from Mycothermus thermophiloides were analyzed for the hydrolysis of biorefinery relevant unwashed pretreated rice straw slurry (PRAJ and IOCL) @17% substrate loading rate.
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Affiliation(s)
- Yashika Raheja
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Varinder Singh
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Baljit Kaur
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Neha Basotra
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Marcos Di Falco
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Adrian Tsang
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
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Hellemann E, Walker JL, Lesko MA, Chandrashekarappa DG, Schmidt MC, O’Donnell AF, Durrant JD. Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics. PLoS Comput Biol 2022; 18:e1009929. [PMID: 35235554 PMCID: PMC8920189 DOI: 10.1371/journal.pcbi.1009929] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/14/2022] [Accepted: 02/16/2022] [Indexed: 01/16/2023] Open
Abstract
Glucose is central to many biological processes, serving as an energy source and a building block for biosynthesis. After glucose enters the cell, hexokinases convert it to glucose-6-phosphate (Glc-6P) for use in anaerobic fermentation, aerobic oxidative phosphorylation, and the pentose-phosphate pathway. We here describe a genetic screen in Saccharomyces cerevisiae that generated a novel spontaneous mutation in hexokinase-2, hxk2G238V, that confers resistance to the toxic glucose analog 2-deoxyglucose (2DG). Wild-type hexokinases convert 2DG to 2-deoxyglucose-6-phosphate (2DG-6P), but 2DG-6P cannot support downstream glycolysis, resulting in a cellular starvation-like response. Curiously, though the hxk2G238V mutation encodes a loss-of-function allele, the affected amino acid does not interact directly with bound glucose, 2DG, or ATP. Molecular dynamics simulations suggest that Hxk2G238V impedes sugar binding by altering the protein dynamics of the glucose-binding cleft, as well as the large-scale domain-closure motions required for catalysis. These findings shed new light on Hxk2 dynamics and highlight how allosteric changes can influence catalysis, providing new structural insights into this critical regulator of carbohydrate metabolism. Given that hexokinases are upregulated in some cancers and that 2DG and its derivatives have been studied in anti-cancer trials, the present work also provides insights that may apply to cancer biology and drug resistance. Glucose fuels many of the energy-production processes required for normal cell growth. Before glucose can participate in these processes, it must first be chemically modified by proteins called hexokinases. To better understand how hexokinases modify glucose—and how mutations in hexokinase genes might confer drug resistance—we evolved resistance in yeast to a toxic hexokinase-binding molecule called 2DG. We discovered a mutation in the hexokinase gene that confers 2DG resistance and reduces the protein’s ability to modify glucose. Biochemical analyses and computer simulations of the hexokinase protein suggest that the mutation diminishes glucose binding by altering enzyme flexibility. This work shows how cells can evolve resistance to toxins via only modest changes to protein structures. Furthermore, because cancer-cell hexokinases are particularly active, 2DG has been studied as cancer chemotherapy. Thus, the insights this work provides might also apply to cancer biology.
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Affiliation(s)
- Erich Hellemann
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jennifer L. Walker
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mitchell A. Lesko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Dakshayini G. Chandrashekarappa
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Martin C. Schmidt
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Allyson F. O’Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (AFO); (JDD)
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (AFO); (JDD)
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Barney JB, Chandrashekarappa DG, Soncini SR, Schmidt MC. Drug resistance in diploid yeast is acquired through dominant alleles, haploinsufficiency, gene duplication and aneuploidy. PLoS Genet 2021; 17:e1009800. [PMID: 34555030 PMCID: PMC8460028 DOI: 10.1371/journal.pgen.1009800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
Previous studies of adaptation to the glucose analog, 2-deoxyglucose, by Saccharomyces cerevisiae have utilized haploid cells. In this study, diploid cells were used in the hope of identifying the distinct genetic mechanisms used by diploid cells to acquire drug resistance. While haploid cells acquire resistance to 2-deoxyglucose primarily through recessive alleles in specific genes, diploid cells acquire resistance through dominant alleles, haploinsufficiency, gene duplication and aneuploidy. Dominant-acting, missense alleles in all three subunits of yeast AMP-activated protein kinase confer resistance to 2-deoxyglucose. Dominant-acting, nonsense alleles in the REG1 gene, which encodes a negative regulator of AMP-activated protein kinase, confer 2-deoxyglucose resistance through haploinsufficiency. Most of the resistant strains isolated in this study achieved resistance through aneuploidy. Cells with a monosomy of chromosome 4 are resistant to 2-deoxyglucose. While this genetic strategy comes with a severe fitness cost, it has the advantage of being readily reversible when 2-deoxyglucose selection is lifted. Increased expression of the two DOG phosphatase genes on chromosome 8 confers resistance and was achieved through trisomies and tetrasomies of that chromosome. Finally, resistance was also mediated by increased expression of hexose transporters, achieved by duplication of a 117 kb region of chromosome 4 that included the HXT3, HXT6 and HXT7 genes. The frequent use of aneuploidy as a genetic strategy for drug resistance in diploid yeast and human tumors may be in part due to its potential for reversibility when selection pressure shifts.
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Affiliation(s)
- Jordan B. Barney
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Dakshayini G. Chandrashekarappa
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Samantha R. Soncini
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Martin C. Schmidt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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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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Endocytosis of nutrient transporters in fungi: The ART of connecting signaling and trafficking. Comput Struct Biotechnol J 2021; 19:1713-1737. [PMID: 33897977 PMCID: PMC8050425 DOI: 10.1016/j.csbj.2021.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/14/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
Plasma membrane transporters play pivotal roles in the import of nutrients, including sugars, amino acids, nucleobases, carboxylic acids, and metal ions, that surround fungal cells. The selective removal of these transporters by endocytosis is one of the most important regulatory mechanisms that ensures a rapid adaptation of cells to the changing environment (e.g., nutrient fluctuations or different stresses). At the heart of this mechanism lies a network of proteins that includes the arrestin‐related trafficking adaptors (ARTs) which link the ubiquitin ligase Rsp5 to nutrient transporters and endocytic factors. Transporter conformational changes, as well as dynamic interactions between its cytosolic termini/loops and with lipids of the plasma membrane, are also critical during the endocytic process. Here, we review the current knowledge and recent findings on the molecular mechanisms involved in nutrient transporter endocytosis, both in the budding yeast Saccharomyces cerevisiae and in some species of the filamentous fungus Aspergillus. We elaborate on the physiological importance of tightly regulated endocytosis for cellular fitness under dynamic conditions found in nature and highlight how further understanding and engineering of this process is essential to maximize titer, rate and yield (TRY)-values of engineered cell factories in industrial biotechnological processes.
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Key Words
- AAs, amino acids
- ACT, amino Acid/Choline Transporter
- AP, adaptor protein
- APC, amino acid-polyamine-organocation
- Arg, arginine
- Arrestins
- Arts, arrestin‐related trafficking adaptors
- Asp, aspartic acid
- Aspergilli
- Biotechnology
- C, carbon
- C-terminus, carboxyl-terminus
- Cell factories
- Conformational changes
- Cu, copper
- DUBs, deubiquitinating enzymes
- EMCs, eisosome membrane compartments
- ER, endoplasmic reticulum
- ESCRT, endosomal sorting complex required for transport
- Endocytic signals
- Endocytosis
- Fe, iron
- Fungi
- GAAC, general amino acid control
- Glu, glutamic acid
- H+, proton
- IF, inward-facing
- LAT, L-type Amino acid Transporter
- LID, loop Interaction Domain
- Lys, lysine
- MCCs, membrane compartments containing the arginine permease Can1
- MCCs/eisosomes
- MCPs, membrane compartments of Pma1
- MFS, major facilitator superfamily
- MVB, multi vesicular bodies
- Met, methionine
- Metabolism
- Mn, manganese
- N, nitrogen
- N-terminus, amino-terminus
- NAT, nucleobase Ascorbate Transporter
- NCS1, nucleobase/Cation Symporter 1
- NCS2, nucleobase cation symporter family 2
- NH4+, ammonium
- Nutrient transporters
- OF, outward-facing
- PEST, proline (P), glutamic acid (E), serine (S), and threonine (T)
- PM, plasma membrane
- PVE, prevacuolar endosome
- Saccharomyces cerevisiae
- Signaling pathways
- Structure-function
- TGN, trans-Golgi network
- TMSs, transmembrane segments
- TORC1, target of rapamycin complex 1
- TRY, titer, rate and yield
- Trp, tryptophan
- Tyr, tyrosine
- Ub, ubiquitin
- Ubiquitylation
- VPS, vacuolar protein sorting
- W/V, weight per volume
- YAT, yeast Amino acid Transporter
- Zn, Zinc
- fAATs, fungal AA transporters
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de Assis LJ, Silva LP, Bayram O, Dowling P, Kniemeyer O, Krüger T, Brakhage AA, Chen Y, Dong L, Tan K, Wong KH, Ries LNA, Goldman GH. Carbon Catabolite Repression in Filamentous Fungi Is Regulated by Phosphorylation of the Transcription Factor CreA. mBio 2021; 12:e03146-20. [PMID: 33402538 PMCID: PMC8545104 DOI: 10.1128/mbio.03146-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Filamentous fungi of the genus Aspergillus are of particular interest for biotechnological applications due to their natural capacity to secrete carbohydrate-active enzymes (CAZy) that target plant biomass. The presence of easily metabolizable sugars such as glucose, whose concentrations increase during plant biomass hydrolysis, results in the repression of CAZy-encoding genes in a process known as carbon catabolite repression (CCR), which is undesired for the purpose of large-scale enzyme production. To date, the C2H2 transcription factor CreA has been described as the major CC repressor in Aspergillus spp., although little is known about the role of posttranslational modifications in this process. In this work, phosphorylation sites were identified by mass spectrometry on Aspergillus nidulans CreA, and subsequently, the previously identified but uncharacterized site S262, the characterized site S319, and the newly identified sites S268 and T308 were chosen to be mutated to nonphosphorylatable residues before their effect on CCR was investigated. Sites S262, S268, and T308 are important for CreA protein accumulation and cellular localization, DNA binding, and repression of enzyme activities. In agreement with a previous study, site S319 was not important for several here-tested phenotypes but is key for CreA degradation and induction of enzyme activities. All sites were shown to be important for glycogen and trehalose metabolism. This study highlights the importance of CreA phosphorylation sites for the regulation of CCR. These sites are interesting targets for biotechnological strain engineering without the need to delete essential genes, which could result in undesired side effects.IMPORTANCE In filamentous fungi, the transcription factor CreA controls carbohydrate metabolism through the regulation of genes encoding enzymes required for the use of alternative carbon sources. In this work, phosphorylation sites were identified on Aspergillus nidulans CreA, and subsequently, the two newly identified sites S268 and T308, the previously identified but uncharacterized site S262, and the previously characterized site S319 were chosen to be mutated to nonphosphorylatable residues before their effect on CCR was characterized. Sites S262, S268, and T308 are important for CreA protein accumulation and cellular localization, DNA binding, and repression of enzyme activities. In agreement with a previous study, site S319 is not important for several here-tested phenotypes but is key for CreA degradation and induction of enzyme activities. This work characterized novel CreA phosphorylation sites under carbon catabolite-repressing conditions and showed that they are crucial for CreA protein turnover, control of carbohydrate utilization, and biotechnologically relevant enzyme production.
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Affiliation(s)
| | - Lilian Pereira Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirao Preto, Brazil
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Ozgur Bayram
- Biology Department, Maynooth University, Maynooth, Kildare, Ireland
| | - Paul Dowling
- Biology Department, Maynooth University, Maynooth, Kildare, Ireland
| | - Olaf Kniemeyer
- Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Thomas Krüger
- Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Axel A Brakhage
- Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Yingying Chen
- Faculty of Health Science, University of Macau, Macau, China
| | - Liguo Dong
- Faculty of Health Science, University of Macau, Macau, China
| | - Kaeling Tan
- Faculty of Health Science, University of Macau, Macau, China
| | - Koon Ho Wong
- Faculty of Health Science, University of Macau, Macau, China
| | - Laure N A Ries
- University of Exeter, MRC Centre for Medical Mycology, Exeter, United Kingdom
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirao Preto, Brazil
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
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11
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Schmidt MC, O'Donnell AF. 'Sugarcoating' 2-deoxyglucose: mechanisms that suppress its toxic effects. Curr Genet 2020; 67:107-114. [PMID: 33136227 PMCID: PMC7886833 DOI: 10.1007/s00294-020-01122-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/06/2020] [Accepted: 10/19/2020] [Indexed: 12/14/2022]
Abstract
Yeast and cancer cells are metabolically similar as they use fermentation of glucose as a primary means of generating energy. Reliance on glucose fermentation makes both of these cell types highly sensitive to the toxic glucose analog, 2-deoxyglucose. Here we review the cellular and metabolic pathways that play a role in 2-deoxyglucose sensitivity and discuss how the modifications to these pathways result in acquisition of 2-deoxyglucose resistance. Insights gained from genetic and proteomic studies in yeast provide new ideas for the design of combinatorial therapies for cancer treatment.
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Affiliation(s)
- Martin C Schmidt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA.
| | - Allyson F O'Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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12
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Laussel C, Léon S. Cellular toxicity of the metabolic inhibitor 2-deoxyglucose and associated resistance mechanisms. Biochem Pharmacol 2020; 182:114213. [PMID: 32890467 DOI: 10.1016/j.bcp.2020.114213] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/31/2022]
Abstract
Most malignant cells display increased glucose absorption and metabolism compared to surrounding tissues. This well-described phenomenon results from a metabolic reprogramming occurring during transformation, that provides the building blocks and supports the high energetic cost of proliferation by increasing glycolysis. These features led to the idea that drugs targeting glycolysis might prove efficient in the context of cancer treatment. One of these drugs, 2-deoxyglucose (2-DG), is a synthetic glucose analog that can be imported into cells and interfere with glycolysis and ATP generation. Its preferential targeting to sites of cell proliferation is supported by the observation that a derived molecule, 2-fluoro-2-deoxyglucose (FDG) accumulates in tumors and is used for cancer imaging. Here, we review the toxicity mechanisms of this drug, from the early-described effects on glycolysis to its other cellular consequences, including inhibition of protein glycosylation and endoplasmic reticulum stress, and its interference with signaling pathways. Then, we summarize the current data on the use of 2-DG as an anti-cancer agent, especially in the context of combination therapies, as novel 2-DG-derived drugs are being developed. We also show how the use of 2-DG helped to decipher glucose-signaling pathways in yeast and favored their engineering for biotechnologies. Finally, we discuss the resistance strategies to this inhibitor that have been identified in the course of these studies and which may have important implications regarding a medical use of this drug.
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Affiliation(s)
- Clotilde Laussel
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France
| | - Sébastien Léon
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France.
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13
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Spontaneous mutations that confer resistance to 2-deoxyglucose act through Hxk2 and Snf1 pathways to regulate gene expression and HXT endocytosis. PLoS Genet 2020; 16:e1008484. [PMID: 32673313 PMCID: PMC7386655 DOI: 10.1371/journal.pgen.1008484] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 07/28/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022] Open
Abstract
Yeast and fast-growing human tumor cells share metabolic similarities in that both cells use fermentation of glucose for energy and both are highly sensitive to the glucose analog 2-deoxyglucose. Spontaneous mutations in S. cerevisiae that conferred resistance to 2-deoxyglucose were identified by whole genome sequencing. Missense alleles of the HXK2, REG1, GLC7 and SNF1 genes were shown to confer significant resistance to 2-deoxyglucose and all had the potential to alter the activity and or target selection of the Snf1 kinase signaling pathway. All three missense alleles in HXK2 resulted in significantly reduced catalytic activity. Addition of 2DG promotes endocytosis of the glucose transporter Hxt3. All but one of the 2DG-resistant strains reduced the 2DG-mediated hexose transporter endocytosis by increasing plasma membrane occupancy of the Hxt3 protein. Increased expression of the DOG (deoxyglucose) phosphatases has been associated with resistance to 2-deoxyglucose. Expression of both the DOG1 and DOG2 mRNA was elevated after treatment with 2-deoxyglucose but induction of these genes is not associated with 2DG-resistance. RNAseq analysis of the transcriptional response to 2DG showed large scale, genome-wide changes in mRNA abundance that were greatly reduced in the 2DG resistant strains. These findings suggest the common adaptive response to 2DG is to limit the magnitude of the response. Genetic studies of 2DG resistance using the dominant SNF1-G53R allele in cells that are genetically compromised in both the endocytosis and DOG pathways suggest that at least one more mechanism for conferring resistance to this glucose analog remains to be discovered. Yeast and fast-growing human tumor cells share metabolic similarities in that both cells use fermentation of glucose for energy and both are highly sensitive to the glucose analog 2-deoxyglucose. Another similarity between yeast cells and human tumor cells is that both cells can acquire resistance to 2-deoxyglucose, an outcome that can limit the usefulness of some cancer therapeutics. In this study, we used bakers’ yeast as a model organism to better understand the mechanism of toxicity and acquisition of resistance to 2-deoxyglucose. Spontaneous mutations in S. cerevisiae that conferred resistance to 2-deoxyglucose were isolated and identified by whole genome sequencing, a technology that was not available until recently. Our studies indicate that 2-deoxyglucose becomes toxic after it is phosphorylated by an enzyme called hexokinase. One important route to resistance is to reduce hexokinase activity. Other parallel pathways to resistance include increased expression of a hydrolase that degrades the toxic metabolite, altered localization of glucose transporters and altered glucose signal transduction pathways.
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14
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Ries LNA, Pardeshi L, Dong Z, Tan K, Steenwyk JL, Colabardini AC, Ferreira Filho JA, de Castro PA, Silva LP, Preite NW, Almeida F, de Assis LJ, dos Santos RAC, Bowyer P, Bromley M, Owens RA, Doyle S, Demasi M, Hernández DCR, Netto LES, Pupo MT, Rokas A, Loures FV, Wong KH, Goldman GH. The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence. PLoS Pathog 2020; 16:e1008645. [PMID: 32667960 PMCID: PMC7384679 DOI: 10.1371/journal.ppat.1008645] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/27/2020] [Accepted: 05/19/2020] [Indexed: 12/21/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic fungal pathogen that secretes an array of immune-modulatory molecules, including secondary metabolites (SMs), which contribute to enhancing fungal fitness and growth within the mammalian host. Gliotoxin (GT) is a SM that interferes with the function and recruitment of innate immune cells, which are essential for eliminating A. fumigatus during invasive infections. We identified a C6 Zn cluster-type transcription factor (TF), subsequently named RglT, important for A. fumigatus oxidative stress resistance, GT biosynthesis and self-protection. RglT regulates the expression of several gli genes of the GT biosynthetic gene cluster, including the oxidoreductase-encoding gene gliT, by directly binding to their respective promoter regions. Subsequently, RglT was shown to be important for virulence in a chemotherapeutic murine model of invasive pulmonary aspergillosis (IPA). Homologues of RglT and GliT are present in eurotiomycete and sordariomycete fungi, including the non-GT-producing fungus A. nidulans, where a conservation of function was described. Phylogenetically informed model testing led to an evolutionary scenario in which the GliT-based resistance mechanism is ancestral and RglT-mediated regulation of GliT occurred subsequently. In conclusion, this work describes the function of a previously uncharacterised TF in oxidative stress resistance, GT biosynthesis and self-protection in both GT-producing and non-producing Aspergillus species.
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Affiliation(s)
- Laure N. A. Ries
- Faculty of Medicine of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Lakhansing Pardeshi
- Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Zhiqiang Dong
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Kaeling Tan
- Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Faculty of Health Sciences, University of Macau, Macau SAR, China
- Centre for Precision Medicine and Research and Training, University of Macau, Macau SAR, China
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
| | - Ana Cristina Colabardini
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Jaire A. Ferreira Filho
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Patricia A. de Castro
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Lilian P. Silva
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Nycolas W. Preite
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Fausto Almeida
- Faculty of Medicine of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Leandro J. de Assis
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Renato A. C. dos Santos
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Paul Bowyer
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Michael Bromley
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | | | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Ireland
| | - Marilene Demasi
- Institute Butantan, Laboratory of Biochemistry and Biophysics, São Paulo, Brazil
| | - Diego C. R. Hernández
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Monica T. Pupo
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
| | - Flavio V. Loures
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Koon H. Wong
- Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Institute of Translational Medicine, University of Macau, Macau SAR, China
| | - Gustavo H. Goldman
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
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15
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da Silva JM, da Silva GHTG, Parente DC, Leite FCB, Silva CS, Valente P, Ganga AM, Simões DA, de Morais MA. Biological diversity of carbon assimilation among isolates of the yeast Dekkera bruxellensis from wine and fuel-ethanol industrial processes. FEMS Yeast Res 2019; 19:5372417. [PMID: 30848782 DOI: 10.1093/femsyr/foz022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 03/07/2019] [Indexed: 12/11/2022] Open
Abstract
Dekkera bruxellensis is considered a spoilage yeast in winemaking, brewing and fuel-ethanol production. However, there is growing evidence in the literature of its biotechnological potential. In this work, we surveyed 29 D. bruxellensis isolates from three countries and two different industrial origins (winemaking and fuel-ethanol production) for the metabolization of industrially relevant sugars. The isolates were characterized by the determination of their maximum specific growth rates, and by testing their ability to grow in the presence of 2-deoxy-d-glucose and antimycin A. Great diversity was observed among the isolates, with fuel-ethanol isolates showing overall higher specific growth rates than wine isolates. Preferences for galactose (three wine isolates) and for cellobiose or lactose (some fuel-ethanol isolates) were observed. Fuel-ethanol isolates were less sensitive than wine isolates to glucose catabolite repression (GCR) induction by 2-deoxy-d-glucose. In strictly anaerobic conditions, isolates selected for having high aerobic growth rates were able to ferment glucose, sucrose and cellobiose at fairly high rates without supplementation of casamino acids or yeast extract in the culture medium. The phenotypic diversity found among wine and fuel-ethanol isolates suggests adaptation to these environments. A possible application of some of the GCR-insensitive, fast-growing isolates in industrial processes requiring co-assimilation of different sugars is considered.
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Affiliation(s)
- Jackeline Maria da Silva
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil.,Department of Biochemistry, Federal University of Pernambuco, Recife, Brazil
| | | | - Denise Castro Parente
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil.,Department of Biochemistry, Federal University of Pernambuco, Recife, Brazil
| | | | - Carolina Santos Silva
- Department of Chemical Engineering, Federal University of Pernambuco, Recife, Brazil
| | - Patrícia Valente
- Department of Microbiology, Immunology and Parasitology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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16
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Tomimoto K, Osafune Y, Kakizono D, Han J, Mukai N. Isolation methods of high glycosidase-producing mutants of Aspergillus luchuensis and its mutated genes. Biosci Biotechnol Biochem 2019; 84:198-207. [PMID: 31566090 DOI: 10.1080/09168451.2019.1671788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
High glycosidase-producing strains of Aspergillus luchuensis were isolated from 2-deoxyglucose (2-DG) resistant mutants. α-Amylase, exo-α-1,4-glucosidase, β-glucosidase and β-xylosidase activity in the mutants was ~3, ~2, ~4 and ~2.5 times higher than the parental strain RIB2604 on koji-making conditions, respectively. Citric acid production and mycelia growth of the mutants, however, approximately halved to that of the parent. Compared to the parent, the alcohol yield from rice and sweet potato shochu mash of the mutant increased ~5.7% and 3.0%, respectively. The mutant strains showed significantly low glucose assimilability despite the fructose one was almost normal, and they had a single missense or nonsense mutation in the glucokinase gene glkA. The recombinant strain that was introduced at one of the mutations, glkA Q300K, demonstrated similar but not identical phenotypes to the mutant strain. This result indicates that glkA Q300K is one of the major mutations in 2-DG resistant strains.
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Affiliation(s)
- Kazuya Tomimoto
- Brewing Microbiology Division, National Research Institute of Brewing, Higashi-hiroshima, Japan
| | - Yukio Osafune
- Brewing Technology Division, National Research Institute of Brewing, Higashi-hiroshima, Japan
| | - Dararat Kakizono
- Brewing Technology Division, National Research Institute of Brewing, Higashi-hiroshima, Japan
| | - Jinshun Han
- Brewing Technology Division, National Research Institute of Brewing, Higashi-hiroshima, Japan
| | - Nobuhiko Mukai
- Brewing Technology Division, National Research Institute of Brewing, Higashi-hiroshima, Japan
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17
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Defenouillère Q, Verraes A, Laussel C, Friedrich A, Schacherer J, Léon S. The induction of HAD-like phosphatases by multiple signaling pathways confers resistance to the metabolic inhibitor 2-deoxyglucose. Sci Signal 2019; 12:12/597/eaaw8000. [PMID: 31481524 DOI: 10.1126/scisignal.aaw8000] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Anti-cancer strategies that target the glycolytic metabolism of tumors have been proposed. The glucose analog 2-deoxyglucose (2DG) is imported into cells and, after phosphorylation, becomes 2DG-6-phosphate, a toxic by-product that inhibits glycolysis. Using yeast as a model, we performed an unbiased mass spectrometry-based approach to probe the cellular effects of 2DG on the proteome and study resistance mechanisms to 2DG. We found that two phosphatases that target 2DG-6-phosphate were induced upon exposure to 2DG and participated in 2DG detoxification. Dog1 and Dog2 are HAD (haloacid dehalogenase)-like phosphatases, which are evolutionarily conserved. 2DG induced Dog2 by activating several signaling pathways, such as the stress response pathway mediated by the p38 MAPK ortholog Hog1, the unfolded protein response (UPR) triggered by 2DG-induced ER stress, and the cell wall integrity (CWI) pathway mediated by the MAPK Slt2. Loss of the UPR or CWI pathways led to 2DG hypersensitivity. In contrast, mutants impaired in the glucose-mediated repression of genes were 2DG resistant because glucose availability transcriptionally repressed DOG2 by inhibiting signaling mediated by the AMPK ortholog Snf1. The characterization and genome resequencing of spontaneous 2DG-resistant mutants revealed that DOG2 overexpression was a common strategy underlying 2DG resistance. The human Dog2 homolog HDHD1 displayed phosphatase activity toward 2DG-6-phosphate in vitro and its overexpression conferred 2DG resistance in HeLa cells, suggesting that this 2DG phosphatase could interfere with 2DG-based chemotherapies. These results show that HAD-like phosphatases are evolutionarily conserved regulators of 2DG resistance.
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Affiliation(s)
- Quentin Defenouillère
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205, Paris Cedex 13, France
| | - Agathe Verraes
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205, Paris Cedex 13, France
| | - Clotilde Laussel
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205, Paris Cedex 13, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
| | - Sébastien Léon
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205, Paris Cedex 13, France.
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18
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Hua Y, Wang J, Zhu Y, Zhang B, Kong X, Li W, Wang D, Hong J. Release of glucose repression on xylose utilization in Kluyveromyces marxianus to enhance glucose-xylose co-utilization and xylitol production from corncob hydrolysate. Microb Cell Fact 2019; 18:24. [PMID: 30709398 PMCID: PMC6359873 DOI: 10.1186/s12934-019-1068-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/20/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Lignocellulosic biomass is one of the most abundant materials for biochemicals production. However, efficient co-utilization of glucose and xylose from the lignocellulosic biomass is a challenge due to the glucose repression in microorganisms. Kluyveromyces marxianus is a thermotolerant and efficient xylose-utilizing yeast. To realize the glucose-xylose co-utilization, analyzing the glucose repression of xylose utilization in K. marxianus is necessary. In addition, a glucose-xylose co-utilization platform strain will facilitate the construction of lignocellulosic biomass-utilizing strains. RESULTS Through gene disruption, hexokinase 1 (KmHXK1) and sucrose non-fermenting 1 (KmSNF1) were proved to be involved in the glucose repression of xylose utilization while disruption of the downstream genes of cyclic AMP-protein kinase A (cAMP-PKA) signaling pathway or sucrose non-fermenting 3 (SNF3) glucose-sensing pathway did not alleviate the repression. Furthermore, disruption of the gene of multicopy inhibitor of GAL gene expression (KmMIG1) alleviated the glucose repression on some nonglucose sugars (galactose, sucrose, and raffinose) but still kept glucose repression of xylose utilization. Real-time PCR analysis of the xylose utilization related genes transcription confirmed these results, and besides, revealed that xylitol dehydrogenase gene (KmXYL2) was the critical gene for xylose utilization and stringently regulated by glucose repression. Many other genes of candidate targets interacting with SNF1 were also evaluated by disruption, but none proved to be the key regulator in the pathway of the glucose repression on xylose utilization. Therefore, there may exist other signaling pathway(s) for glucose repression on xylose consumption. Based on these results, a thermotolerant xylose-glucose co-consumption platform strain of K. marxianus was constructed. Then, exogenous xylose reductase and xylose-specific transporter genes were overexpressed in the platform strain to obtain YHY013. The YHY013 could efficiently co-utilized the glucose and xylose from corncob hydrolysate or xylose mother liquor for xylitol production (> 100 g/L) even with inexpensive organic nitrogen sources. CONCLUSIONS The analysis of the glucose repression in K. marxianus laid the foundation for construction of the glucose-xylose co-utilizing platform strain. The efficient xylitol production strain further verified the potential of the platform strain in exploitation of lignocellulosic biomass.
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Affiliation(s)
- Yan Hua
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, 230026, Anhui, People's Republic of China
| | - Jichao Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yelin Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Biao Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Xin Kong
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, 230026, Anhui, People's Republic of China
| | - Wenjie Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, 230026, Anhui, People's Republic of China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, 230026, Anhui, People's Republic of China.
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19
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AMPK-Mediated Regulation of Alpha-Arrestins and Protein Trafficking. Int J Mol Sci 2019; 20:ijms20030515. [PMID: 30691068 PMCID: PMC6387238 DOI: 10.3390/ijms20030515] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 12/18/2022] Open
Abstract
The adenosine monophosphate-activated protein kinase (AMPK) plays a central role in the regulation of cellular metabolism. Recent studies reveal a novel role for AMPK in the regulation of glucose and other carbohydrates flux by controlling the endocytosis of transporters. The first step in glucose metabolism is glucose uptake, a process mediated by members of the GLUT/SLC2A (glucose transporters) or HXT (hexose transporters) family of twelve-transmembrane domain glucose transporters in mammals and yeast, respectively. These proteins are conserved from yeast to humans, and multiple transporters—each with distinct kinetic properties—compete for plasma membrane occupancy in order to enhance or limit the rate of glucose uptake. During growth in the presence of alternative carbon sources, glucose transporters are removed and replaced with the appropriate transporter to help support growth in response to this environment. New insights into the regulated protein trafficking of these transporters reveal the requirement for specific α-arrestins, a little-studied class of protein trafficking adaptor. A defining feature of the α-arrestins is that each contains PY-motifs, which can bind to the ubiquitin ligases from the NEDD4/Rsp5 (Neural precursor cell Expressed, Developmentally Down-regulated 4 and Reverses Spt- Phenotype 5, respectively) family. Specific association of α-arrestins with glucose and carbohydrate transporters is thought to bring the ubiquitin ligase in close proximity to its membrane substrate, and thereby allows the membrane cargo to become ubiquitinated. This ubiquitination in turn serves as a mark to stimulate endocytosis. Recent results show that AMPK phosphorylation of the α-arrestins impacts their abundance and/or ability to stimulate carbohydrate transporter endocytosis. Indeed, AMPK or glucose limitation also controls α-arrestin gene expression, adding an additional layer of complexity to this regulation. Here, we review the recent studies that have expanded the role of AMPK in cellular metabolism to include regulation of α-arrestin-mediated trafficking of transporters and show that this mechanism of regulation is conserved over the ~150 million years of evolution that separate yeast from man.
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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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Gibney PA, Schieler A, Chen JC, Bacha-Hummel JM, Botstein M, Volpe M, Silverman SJ, Xu Y, Bennett BD, Rabinowitz JD, Botstein D. Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast. Mol Biol Cell 2018; 29:897-910. [PMID: 29444955 PMCID: PMC5896929 DOI: 10.1091/mbc.e17-11-0666] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Metabolic dysregulation leading to sugar-phosphate accumulation is toxic in organisms ranging from bacteria to humans. By comparing two models of sugar-phosphate toxicity in Saccharomyces cerevisiae, we demonstrate that toxicity occurs, at least in part, through multiple, isomer-specific mechanisms, rather than a single general mechanism.
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Affiliation(s)
- Patrick A Gibney
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Ariel Schieler
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Jonathan C Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Maxim Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Matthew Volpe
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Sanford J Silverman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Yifan Xu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
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22
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Le Pogam P, Doué M, Le Page Y, Habauzit D, Zhadobov M, Sauleau R, Le Dréan Y, Rondeau D. Untargeted Metabolomics Reveal Lipid Alterations upon 2-Deoxyglucose Treatment in Human HaCaT Keratinocytes. J Proteome Res 2018; 17:1146-1157. [PMID: 29430917 DOI: 10.1021/acs.jproteome.7b00805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The glucose analogue 2-deoxyglucose (2-DG) impedes cancer progression in animal models and is currently being assessed as an anticancer therapy, yet the mode of action of this drug of high clinical significance has not been fully delineated. In an attempt to better characterize its pharmacodynamics, an integrative UPLC-Q-Exactive-based joint metabolomic and lipidomic approach was undertaken to evaluate the metabolic perturbations induced by this drug in human HaCaT keratinocyte cells. R-XCMS data processing and subsequent multivariate pattern recognition, metabolites identification, and pathway analyses identified eight metabolites that were most significantly changed upon a 3 h 2-DG exposure. Most of these dysregulated features were emphasized in the course of lipidomic profiling and could be identified as ceramide and glucosylceramide derivatives, consistently with their involvement in cell death programming. Even though metabolomic analyses did not generally afford such clear-cut dysregulations, some alterations in phosphatidylcholine and phosphatidylethanolamine derivatives could be highlighted as well. Overall, these results support the adequacy of the proposed analytical workflow and might contribute to a better understanding of the mechanisms underlying the promising effects of 2-DG.
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Affiliation(s)
- Pierre Le Pogam
- Institute of Electronics and Telecommunications of Rennes (IETR), UMR CNRS 6164, University of Rennes , Campus de Beaulieu, 263 avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Mickael Doué
- Institute of Electronics and Telecommunications of Rennes (IETR), UMR CNRS 6164, University of Rennes , Campus de Beaulieu, 263 avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Yann Le Page
- Transcription, Environment and Cancer Group, Institute for Research on Environmental and Occupational Health (IRSET), Inserm UMR1085, University of Rennes 1 , 9 avenue du Prof. Léon Bernard, 35043 Rennes Cedex, France
| | - Denis Habauzit
- Transcription, Environment and Cancer Group, Institute for Research on Environmental and Occupational Health (IRSET), Inserm UMR1085, University of Rennes 1 , 9 avenue du Prof. Léon Bernard, 35043 Rennes Cedex, France
| | - Maxim Zhadobov
- Institute of Electronics and Telecommunications of Rennes (IETR), UMR CNRS 6164, University of Rennes , Campus de Beaulieu, 263 avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Ronan Sauleau
- Institute of Electronics and Telecommunications of Rennes (IETR), UMR CNRS 6164, University of Rennes , Campus de Beaulieu, 263 avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Yves Le Dréan
- Transcription, Environment and Cancer Group, Institute for Research on Environmental and Occupational Health (IRSET), Inserm UMR1085, University of Rennes 1 , 9 avenue du Prof. Léon Bernard, 35043 Rennes Cedex, France
| | - David Rondeau
- Institute of Electronics and Telecommunications of Rennes (IETR), UMR CNRS 6164, University of Rennes , Campus de Beaulieu, 263 avenue du Général Leclerc, 35042 Rennes Cedex, France.,Département de Chimie, Université de Bretagne Occidentale , 6 avenue Victor Le Gorgeu, 29238 Brest Cedex, France
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23
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Adamczyk M, Szatkowska R. Low RNA Polymerase III activity results in up regulation of HXT2 glucose transporter independently of glucose signaling and despite changing environment. PLoS One 2017; 12:e0185516. [PMID: 28961268 PMCID: PMC5621690 DOI: 10.1371/journal.pone.0185516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/14/2017] [Indexed: 01/13/2023] Open
Abstract
Background Saccharomyces cerevisiae responds to glucose availability in the environment, inducing the expression of the low-affinity transporters and high-affinity transporters in a concentration dependent manner. This cellular decision making is controlled through finely tuned communication between multiple glucose sensing pathways including the Snf1-Mig1, Snf3/Rgt2-Rgt1 (SRR) and cAMP-PKA pathways. Results We demonstrate the first evidence that RNA Polymerase III (RNAP III) activity affects the expression of the glucose transporter HXT2 (RNA Polymerase II dependent—RNAP II) at the level of transcription. Down-regulation of RNAP III activity in an rpc128-1007 mutant results in a significant increase in HXT2 mRNA, which is considered to respond only to low extracellular glucose concentrations. HXT2 expression is induced in the mutant regardless of the growth conditions either at high glucose concentration or in the presence of a non-fermentable carbon source such as glycerol. Using chromatin immunoprecipitation (ChIP), we found an increased association of Rgt1 and Tup1 transcription factors with the highly activated HXT2 promoter in the rpc128-1007 strain. Furthermore, by measuring cellular abundance of Mth1 corepressor, we found that in rpc128-1007, HXT2 gene expression was independent from Snf3/Rgt2-Rgt1 (SRR) signaling. The Snf1 protein kinase complex, which needs to be active for the release from glucose repression, also did not appear perturbed in the mutated strain. Conclusions/Significance These findings suggest that the general activity of RNAP III can indirectly affect the RNAP II transcriptional machinery on the HXT2 promoter when cellular perception transduced via the major signaling pathways, broadly recognized as on/off switch essential to either positive or negative HXT gene regulation, remain entirely intact. Further, Rgt1/Ssn6-Tup1 complex, which has a dual function in gene transcription as a repressor-activator complex, contributes to HXT2 transcriptional activation.
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Affiliation(s)
- Malgorzata Adamczyk
- Institute of Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
- * E-mail:
| | - Roza Szatkowska
- Institute of Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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24
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Vishwanatha A, D'Souza CJM, Schweingruber ME. Genes Controlling 2-deoxyglucose Induced Lysis and Formation of Reactive Oxygen Species in Schizosaccharomyces pombe. Pol J Microbiol 2017; 66:393-396. [PMID: 29319508 DOI: 10.5604/01.3001.0010.4877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Schizosaccharomyces pombe cells of strains each carrying a deletion of one of the genes snf5, ypa1, pho7 and pas1 and of a strain overexpressing gene odr1, have been previously shown to grow in presence of the toxic glucose analogue 2-deoxyglucose (2-DG). Here we report that these genes control 2-DG induced lysis and are, with the exception of odr1, also involved in control of formation of reactive oxygen species (ROS) upon exposure of cells to H2O2. Lysis of deletion strains, but not of strain overexpressing odr1, is dependent on glucose concentration of the medium whereas ROS formation is glucose independent.
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Affiliation(s)
- Akshay Vishwanatha
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru, Karnataka, India
| | - Cletus J M D'Souza
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru, Karnataka, India
| | - Martin E Schweingruber
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru, Karnataka, India
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25
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Lima JO, Pereira JF, Araújo EFD, Queiroz MVD. Pectin lyase overproduction by Penicillium griseoroseum mutants resistant to catabolite repression. Braz J Microbiol 2017; 48:602-606. [PMID: 28237679 PMCID: PMC5498439 DOI: 10.1016/j.bjm.2016.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 12/09/2016] [Accepted: 12/26/2016] [Indexed: 12/30/2022] Open
Abstract
Expression of pectinolytic genes is regulated by catabolic repression limiting the production of pectin lyase (PL) if the natural inducer, pectin, is missing from the growth medium. Here, we report the isolation of Penicillium griseoroseum mutants resistant to 2-deoxy-d-glucose (DG) that show resistance to catabolite repression and overproduce PL. Three spontaneous and nine UV-induced mutants were obtained. Some mutants produced sectors (segments morphologically different) that were also studied. The mutants were analyzed for pectinases production on pectinase-agar plates and five mutants and two sectors showing larger clearing zones than the wild type were selected for quantitative assay. Although PL production higher than the wild type has been found, phenotype instability was observed for most of the mutants and, after transfers to nonselective medium, the DG resistance was no longer present. Only mutants M03 and M04 were stable maintaining the DG-resistance phenotype. When growing for 120 h in liquid medium containing glucose with or without pectin, both mutants showed higher PL production. In the presence of glucose as sole carbon source, the mutant M03 produced 7.8-fold more PL than the wild type. Due its phenotypic stability and PL overproduction, the mutant M03 presents potential for industrial applications.
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Affiliation(s)
| | - Jorge Fernando Pereira
- Universidade Federal de Viçosa, Departamento de Microbiologia, Viçosa, MG, Brazil; Embrapa Trigo, Passo Fundo, RS, Brazil
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26
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Vishwanatha A, D'Souza CJM. Multifaceted effects of antimetabolite and anticancer drug, 2-deoxyglucose on eukaryotic cancer models budding and fission yeast. IUBMB Life 2017; 69:137-147. [DOI: 10.1002/iub.1599] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/20/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Akshay Vishwanatha
- Department of Studies in Biochemistry; University of Mysore; Manasagangotri Mysore Karnataka India
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27
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Vishwanatha A, Rallis C, Bevkal Subramanyaswamy S, D'Souza CJM, Bähler J, Schweingruber ME. Identification of nuclear genes affecting 2-Deoxyglucose resistance in Schizosaccharomyces pombe. FEMS Yeast Res 2016; 16:fow061. [PMID: 27481777 PMCID: PMC5452730 DOI: 10.1093/femsyr/fow061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 01/16/2023] Open
Abstract
2-Deoxyglucose (2-DG) is a toxic glucose analog. To identify genes involved in 2-DG toxicity in Schizosaccharomyces pombe, we screened a wild-type overexpression library for genes which render cells 2-DG resistant. A gene we termed odr1, encoding an uncharacterized hydrolase, led to strong resistance and altered invertase expression when overexpressed. We speculate that Odr1 neutralizes the toxic form of 2-DG, similar to the Saccharomyces cerevisiae Dog1 and Dog2 phosphatases which dephosphorylate 2-DG-6-phosphate synthesized by hexokinase. In a complementary approach, we screened a haploid deletion library to identify 2-DG-resistant mutants. This screen identified the genes snf5, ypa1, pas1 and pho7. In liquid medium, deletions of these genes conferred 2-DG resistance preferentially under glucose-repressed conditions. The deletion mutants expressed invertase activity more constitutively than the control strain, indicating defects in the control of glucose repression. No S. cerevisiae orthologs of the pho7 gene is known, and no 2-DG resistance has been reported for any of the deletion mutants of the other genes identified here. Moreover, 2-DG leads to derepressed invertase activity in S. pombe, while in S. cerevisiae it becomes repressed. Taken together, these findings suggest that mechanisms involved in 2-DG resistance differ between budding and fission yeasts.
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Affiliation(s)
- Akshay Vishwanatha
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India
| | - Charalampos Rallis
- Research Department of Genetics, Evolution and Environment, UCL Institute of Healthy Ageing, University College London, London WC1E 6BT, UK
| | - Shubha Bevkal Subramanyaswamy
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012 Bern, Switzerland
| | | | - Jürg Bähler
- Research Department of Genetics, Evolution and Environment, UCL Institute of Healthy Ageing, University College London, London WC1E 6BT, UK
| | - Martin Ernst Schweingruber
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru 570 006, Karnataka, India
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28
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Mukherjee S, Chandrababunaidu MM, Panda A, Khowala S, Tripathy S. Tricking Arthrinium malaysianum into Producing Industrially Important Enzymes Under 2-Deoxy D-Glucose Treatment. Front Microbiol 2016; 7:596. [PMID: 27242677 PMCID: PMC4865484 DOI: 10.3389/fmicb.2016.00596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/11/2016] [Indexed: 01/24/2023] Open
Abstract
This study catalogs production of industrially important enzymes and changes in transcript expression caused by 2-deoxy D-glucose (2-DG) treatment in Arthrinium malaysianum cultures. Carbon Catabolite Repression (CCR) induced by 2-DG in this species is cAMP independent unlike many other organisms. Higher levels of secreted endoglucanase (EG), β-glucosidase (BGL), β-xylosidase (BXL), and filter paper activity assay (FPase) enzymes under 2-DG treatment can be exploited for commercial purposes. An integrated RNA sequencing and quantitative proteomic analysis was performed to investigate the cellular response to 2-DG in A. malaysianum. Analysis of RNASeq data under 2-DG treated and control condition reveals that 56% of the unigenes do not have any known similarity to proteins in non-redundant database. Gene Ontology IDs were assigned to 36% of the transcripts (13260) and about 5207 (14%) were mapped to Kyoto Encyclopedia of Genes and Genomes pathway (KEGG). About 1711 genes encoding 2691 transcripts were differentially expressed in treated vs. control samples. Out of the 2691 differentially expressed transcripts, only 582 have any known function. The most up regulated genes belonged to Pentose Phosphate Pathways and carbohydrate degradation class as expected. In addition, genes involved in protein folding, binding, catalytic activity, DNA repair, and secondary metabolites were up-regulated under 2-DG treatment. Whereas genes encoding glycosylation pathways, growth, nutrient reservoir activity was repressed. Gene ontology analysis of the differentially expressed genes indicates metabolic process (35%) is the pre-dominant class followed by carbohydrate degradation (11%), protein folding, and trafficking (6.2%) and transport (5.3%) classes. Unlike other organisms, conventional unfolded protein response (UPR) was not activated in either control or treated conditions. Major enzymes secreted by A. malaysianum are those degrading plant polysaccharides, the most dominant ones being β-glucosidase, as demonstrated by the 2D gel analysis. A set of 7 differentially expressed mRNAs were validated by qPCR. Transmission electron microscopy analyses demonstrated that the 2-DG treated cell walls of hyphae showed significant differences in the cell-wall thickness. Overall 2-DG treatment in A. malaysianum induced secretion of large amount of commercially viable enzymes compared to other known species.
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Affiliation(s)
- Soumya Mukherjee
- Drug Development Diagnostic and Biotechnology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Mathu Malar Chandrababunaidu
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Arijit Panda
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Suman Khowala
- Drug Development Diagnostic and Biotechnology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Sucheta Tripathy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
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29
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Hübscher V, Mudholkar K, Chiabudini M, Fitzke E, Wölfle T, Pfeifer D, Drepper F, Warscheid B, Rospert S. The Hsp70 homolog Ssb and the 14-3-3 protein Bmh1 jointly regulate transcription of glucose repressed genes in Saccharomyces cerevisiae. Nucleic Acids Res 2016; 44:5629-45. [PMID: 27001512 PMCID: PMC4937304 DOI: 10.1093/nar/gkw168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 03/03/2016] [Indexed: 11/26/2022] Open
Abstract
Chaperones of the Hsp70 family interact with a multitude of newly synthesized polypeptides and prevent their aggregation. Saccharomyces cerevisiae cells lacking the Hsp70 homolog Ssb suffer from pleiotropic defects, among others a defect in glucose-repression. The highly conserved heterotrimeric kinase SNF1/AMPK (AMP-activated protein kinase) is required for the release from glucose-repression in yeast and is a key regulator of energy balance also in mammalian cells. When glucose is available the phosphatase Glc7 keeps SNF1 in its inactive, dephosphorylated state. Dephosphorylation depends on Reg1, which mediates targeting of Glc7 to its substrate SNF1. Here we show that the defect in glucose-repression in the absence of Ssb is due to the ability of the chaperone to bridge between the SNF1 and Glc7 complexes. Ssb performs this post-translational function in concert with the 14-3-3 protein Bmh, to which Ssb binds via its very C-terminus. Raising the intracellular concentration of Ssb or Bmh enabled Glc7 to dephosphorylate SNF1 even in the absence of Reg1. By that Ssb and Bmh efficiently suppressed transcriptional deregulation of Δreg1 cells. The findings reveal that Ssb and Bmh comprise a new chaperone module, which is involved in the fine tuning of a phosphorylation-dependent switch between respiration and fermentation.
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Affiliation(s)
- Volker Hübscher
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, D-79104 Freiburg, Germany
| | - Kaivalya Mudholkar
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, D-79104 Freiburg, Germany
| | - Marco Chiabudini
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, D-79104 Freiburg, Germany BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Edith Fitzke
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, D-79104 Freiburg, Germany
| | - Tina Wölfle
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, D-79104 Freiburg, Germany
| | - Dietmar Pfeifer
- Genomics Lab, Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center, University of Freiburg, D-79106 Freiburg, Germany
| | - Friedel Drepper
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany Department of Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Bettina Warscheid
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany Department of Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, D-79104 Freiburg, Germany BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
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30
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Differential Phosphorylation Provides a Switch to Control How α-Arrestin Rod1 Down-regulates Mating Pheromone Response in Saccharomyces cerevisiae. Genetics 2016; 203:299-317. [PMID: 26920760 PMCID: PMC4858781 DOI: 10.1534/genetics.115.186122] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/22/2016] [Indexed: 12/20/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) are integral membrane proteins that initiate stimulus-dependent activation of cognate heterotrimeric G-proteins, triggering ensuing downstream cellular responses. Tight regulation of GPCR-evoked pathways is required because prolonged stimulation can be detrimental to an organism. Ste2, a GPCR in Saccharomyces cerevisiae that mediates response of MATa haploids to the peptide mating pheromone α-factor, is down-regulated by both constitutive and agonist-induced endocytosis. Efficient agonist-stimulated internalization of Ste2 requires its association with an adaptor protein, the α-arrestin Rod1/Art4, which recruits the HECT-domain ubiquitin ligase Rsp5, allowing for ubiquitinylation of the C-terminal tail of the receptor and its engagement by the clathrin-dependent endocytic machinery. We previously showed that dephosphorylation of Rod1 by calcineurin (phosphoprotein phosphatase 2B) is required for optimal Rod1 function in Ste2 down-regulation. We show here that negative regulation of Rod1 by phosphorylation is mediated by two distinct stress-activated protein kinases, Snf1/AMPK and Ypk1/SGK1, and demonstrate both in vitro and in vivo that this phospho-regulation impedes the ability of Rod1 to promote mating pathway desensitization. These studies also revealed that, in the absence of its phosphorylation, Rod1 can promote adaptation independently of Rsp5-mediated receptor ubiquitinylation, consistent with recent evidence that α-arrestins can contribute to cargo recognition by both clathrin-dependent and clathrin-independent mechanisms. However, in cells lacking a component (formin Bni1) required for clathrin-independent entry, Rod1 derivatives that are largely unphosphorylated and unable to associate with Rsp5 still promote efficient adaptation, indicating a third mechanism by which this α-arrestin promotes desensitization of the pheromone-response pathway.
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31
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The INO80 Complex Requires the Arp5-Ies6 Subcomplex for Chromatin Remodeling and Metabolic Regulation. Mol Cell Biol 2016; 36:979-91. [PMID: 26755556 DOI: 10.1128/mcb.00801-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/30/2015] [Indexed: 11/20/2022] Open
Abstract
ATP-dependent chromatin remodeling complexes are essential for transcription regulation, and yet it is unclear how these multisubunit complexes coordinate their activities to facilitate diverse transcriptional responses. In this study, we found that the conserved Arp5 and Ies6 subunits of the Saccharomyces cerevisiae INO80 chromatin-remodeler form an abundant and distinct subcomplex in vivo and stimulate INO80-mediated activity in vitro. Moreover, our genomic studies reveal that the relative occupancy of Arp5-Ies6 correlates with nucleosome positioning at transcriptional start sites and expression levels of >1,000 INO80-regulated genes. Notably, these genes are significantly enriched in energy metabolism pathways. Specifically, arp5Δ, ies6Δ, and ino80Δ mutants demonstrate decreased expression of genes involved in glycolysis and increased expression of genes in the oxidative phosphorylation pathway. Deregulation of these metabolic pathways results in constitutively elevated mitochondrial potential and oxygen consumption. Our results illustrate the dynamic nature of the INO80 complex assembly and demonstrate for the first time that a chromatin remodeler regulates glycolytic and respiratory capacity, thereby maintaining metabolic stability.
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32
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Barros de Souza R, Silva RK, Ferreira DS, de Sá Leitão Paiva Junior S, de Barros Pita W, de Morais Junior MA. Magnesium ions in yeast: setting free the metabolism from glucose catabolite repression. Metallomics 2016; 8:1193-1203. [DOI: 10.1039/c6mt00157b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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2-Deoxyglucose impairs Saccharomyces cerevisiae growth by stimulating Snf1-regulated and α-arrestin-mediated trafficking of hexose transporters 1 and 3. Mol Cell Biol 2014; 35:939-55. [PMID: 25547292 DOI: 10.1128/mcb.01183-14] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The glucose analog 2-deoxyglucose (2DG) inhibits the growth of Saccharomyces cerevisiae and human tumor cells, but its modes of action have not been fully elucidated. Yeast cells lacking Snf1 (AMP-activated protein kinase) are hypersensitive to 2DG. Overexpression of either of two low-affinity, high-capacity glucose transporters, Hxt1 and Hxt3, suppresses the 2DG hypersensitivity of snf1Δ cells. The addition of 2DG or the loss of Snf1 reduces HXT1 and HXT3 expression levels and stimulates transporter endocytosis and degradation in the vacuole. 2DG-stimulated trafficking of Hxt1 and Hxt3 requires Rod1/Art4 and Rog3/Art7, two members of the α-arrestin trafficking adaptor family. Mutations in ROD1 and ROG3 that block binding to the ubiquitin ligase Rsp5 eliminate Rod1- and Rog3-mediated trafficking of Hxt1 and Hxt3. Genetic analysis suggests that Snf1 negatively regulates both Rod1 and Rog3, but via different mechanisms. Snf1 activated by 2DG phosphorylates Rod1 but fails to phosphorylate other known targets, such as the transcriptional repressor Mig1. We propose a novel mechanism for 2DG-induced toxicity whereby 2DG stimulates the modification of α-arrestins, which promote glucose transporter internalization and degradation, causing glucose starvation even when cells are in a glucose-rich environment.
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