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Isoda T, Takeda E, Hosokawa S, Hotta-Ren S, Ohsumi Y. Atg45 is an autophagy receptor for glycogen, a non-preferred cargo of bulk autophagy in yeast. iScience 2024; 27:109810. [PMID: 38832010 PMCID: PMC11145338 DOI: 10.1016/j.isci.2024.109810] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 04/22/2024] [Indexed: 06/05/2024] Open
Abstract
The mechanisms governing autophagy of proteins and organelles have been well studied, but how other cytoplasmic components such as RNA and polysaccharides are degraded remains largely unknown. In this study, we examine autophagy of glycogen, a storage form of glucose. We find that cells accumulate glycogen in the cytoplasm during nitrogen starvation and that this carbohydrate is rarely observed within autophagosomes and autophagic bodies. However, sequestration of glycogen by autophagy is observed following prolonged nitrogen starvation. We identify a yet-uncharacterized open reading frame, Yil024c (herein Atg45), as encoding a cytosolic receptor protein that mediates autophagy of glycogen (glycophagy). Furthermore, we show that, during sporulation, Atg45 is highly expressed and is associated with an increase in glycophagy. Our results suggest that cells regulate glycophagic activity by controlling the expression level of Atg45.
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Affiliation(s)
- Takahiro Isoda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Frontier Research Center, POLA Chemical Industries, Inc, Yokohama 244-0812, Japan
| | - Eigo Takeda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Sachiko Hosokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Shukun Hotta-Ren
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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2
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Valorization of Spent Brewer’s Yeast for the Production of High-Value Products, Materials, and Biofuels and Environmental Application. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9030208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Spent brewer’s yeast (SBY) is a byproduct of the brewing industry traditionally used as a feed additive, although it could have much broader applications. In this paper, a comprehensive review of valorization of SBY for the production of high-value products, new materials, and biofuels, as well as environmental application, is presented. An economic perspective is given by mirroring marketing of conventional SBY with innovative high-value products. Cascading utilization of fine chemicals, biofuels, and nutrients such as proteins, carbohydrates, and lipids released by various SBY treatments has been proposed as a means to maximize the sustainable and circular economy.
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Chapela SP, Burgos HI, Stella CA. N-Acetyl cysteine improves cellular growth in respiratory-deficient yeast. Braz J Microbiol 2022; 53:791-794. [PMID: 35122656 PMCID: PMC9151961 DOI: 10.1007/s42770-022-00705-5] [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: 10/18/2021] [Accepted: 02/01/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Reactive oxygen species (ROS) is a main factor that alters cellular physiology and functionality. Many strategies are used in order to control excessive oxidative stress. One strategy includes the use of antioxidants like N-acetyl cysteine (NAC). The aim of this study was to compare the effect of this antioxidant on ROS production and cellular growth of a wild-type and a respiratory-deficient Saccharomyces cerevisiae strain. METHODS Using a simple system such as yeast allows oxidative stress investigations on which numerous factors are more manageable or circumscribed than in a higher organism. We grew cells in a complex medium and incubated them during 72 h. Later, cellular viability and ROS production was evaluated. ROS level was estimated by use of fluorescence signal with 2',7'-dichlorofluorescein diacetate (DCFH-DA). RESULTS As it is found in the present work, a reducing environment exerted by NAC presence during incubation of the cells allows a respiratory-deficient Saccharomyces cerevisiae strain to improve its cellular growth. CONCLUSIONS It seems likely that the energy production or the phenotype which characterizes a deficient strain is incapable of palliating ROS growth inhibition while NAC helps to overcome this limitation.
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Affiliation(s)
- Sebastián P. Chapela
- grid.414382.80000 0001 2337 0926Hospital Británico Buenos Aires, CABA, Buenos Aires, Argentina ,grid.7345.50000 0001 0056 1981Facultad de Medicina, Instituto de Investigaciones Biomédicas (INBIOMED), Buenos Aires, Argentina
| | - Hilda I. Burgos
- grid.7345.50000 0001 0056 1981Facultad de Medicina, Instituto de Investigaciones Biomédicas (INBIOMED), Buenos Aires, Argentina
| | - Carlos A. Stella
- grid.7345.50000 0001 0056 1981Facultad de Medicina, Instituto de Investigaciones Biomédicas (INBIOMED), Buenos Aires, Argentina
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4
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Li Y, Tian C, Liu K, Zhou Y, Yang J, Zou P. A Clickable APEX Probe for Proximity-Dependent Proteomic Profiling in Yeast. Cell Chem Biol 2020; 27:858-865.e8. [DOI: 10.1016/j.chembiol.2020.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/24/2019] [Accepted: 05/08/2020] [Indexed: 10/24/2022]
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Abstract
Glycogen, the primary storage form of glucose, is a rapid and accessible form of energy that can be supplied to tissues on demand. Each glycogen granule, or "glycosome," is considered an independent metabolic unit composed of a highly branched polysaccharide and various proteins involved in its metabolism. In this Minireview, we review the literature to follow the dynamic life of a glycogen granule in a multicompartmentalized system, i.e. the cell, and how and where glycogen granules appear and the factors governing its degradation. A better understanding of the importance of cellular compartmentalization as a regulator of glycogen metabolism is needed to unravel its role in brain energetics.
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Affiliation(s)
- Clara Prats
- Center for Healthy Aging, Copenhagen 2200, Denmark; Core Facility for Integrated Microscopy, Department of Biomedical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
| | - Terry E Graham
- Department of Human Health and Nutritional Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jane Shearer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Calgary, Alberta T2N 1N4, Canada; Faculty of Kinesiology, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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Masuo S, Komatsuzaki A, Takeshita N, Itoh E, Takaaki O, Zhou S, Takaya N. Spatial heterogeneity of glycogen and its metabolizing enzymes in Aspergillus nidulans hyphal tip cells. Fungal Genet Biol 2017; 110:48-55. [PMID: 29175367 DOI: 10.1016/j.fgb.2017.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 11/18/2017] [Accepted: 11/22/2017] [Indexed: 01/13/2023]
Abstract
Glycogen is a homopolymer of glucose and a ubiquitous cellular-storage carbon. This study investigated which Aspergillus nidulans genes are involved in glycogen metabolism. Gene disruptants of predicted glycogen synthase (gsyA) and glycogenin (glgA) genes accumulated less cellular glycogen than the wild type strain, indicating that GsyA and GlgA synthesize glycogen similarly to other eukaryotes. Meanwhile, gene disruption of gphA encoding glycogen phosphorylase increased the amount of glycogen to a higher degree than wild type during the stationary phase that accompanies carbon-source limitation. GFP-tagged GsyA and GphA were distributed in the cytosol and formed punctate and filamentous structures, respectively. Carbon starvation resulted in elongated GphA-GFP filaments and increased numbers of filaments. These structures were more frequently located in the basal regions of tip cells and adjacent cells than in the apical regions of tip cells. Cellular glycogen visualized by incorporation of a fluorescent glucose analog accumulated in cytoplasmic puncta that were more prevalent in the basal regions, a pattern similar to that seen for GsyA. The colocalization of glycogen and GsyA at punctate structures in tip and sub-apical cells likely represents the cellular machinery for synthesizing glycogen. More frequent colocalization in the basal, rather than tip cell apical regions indicated that tip cells have differentiated subcellular regions for glycogen synthesis. Our findings regarding glycogen, GsyA and GphA distribution evoke the spatial heterogeneity of glycogen metabolism in fungal hyphae.
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Affiliation(s)
- Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Airi Komatsuzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Norio Takeshita
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Eriko Itoh
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Okazoe Takaaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Shengmin Zhou
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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Mahalingan KK, Baskaran S, DePaoli-Roach AA, Roach PJ, Hurley TD. Redox Switch for the Inhibited State of Yeast Glycogen Synthase Mimics Regulation by Phosphorylation. Biochemistry 2016; 56:179-188. [PMID: 27935293 DOI: 10.1021/acs.biochem.6b00884] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Glycogen synthase (GS) is the rate limiting enzyme in the synthesis of glycogen. Eukaryotic GS is negatively regulated by covalent phosphorylation and allosterically activated by glucose-6-phosphate (G-6-P). To gain structural insights into the inhibited state of the enzyme, we solved the crystal structure of yGsy2-R589A/R592A to a resolution of 3.3 Å. The double mutant has an activity ratio similar to the phosphorylated enzyme and also retains the ability to be activated by G-6-P. When compared to the 2.88 Å structure of the wild-type G-6-P activated enzyme, the crystal structure of the low-activity mutant showed that the N-terminal domain of the inhibited state is tightly held against the dimer-related interface thereby hindering acceptor access to the catalytic cleft. On the basis of these two structural observations, we developed a reversible redox regulatory feature in yeast GS by substituting cysteine residues for two highly conserved arginine residues. When oxidized, the cysteine mutant enzyme exhibits activity levels similar to the phosphorylated enzyme but cannot be activated by G-6-P. Upon reduction, the cysteine mutant enzyme regains normal activity levels and regulatory response to G-6-P activation.
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Affiliation(s)
- Krishna K Mahalingan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
| | - Sulochanadevi Baskaran
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
| | - Anna A DePaoli-Roach
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
| | - Peter J Roach
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
| | - Thomas D Hurley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
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8
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Analysis of transcriptional profiles of Saccharomyces cerevisiae exposed to bisphenol A. Curr Genet 2016; 63:253-274. [DOI: 10.1007/s00294-016-0633-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/14/2016] [Accepted: 07/16/2016] [Indexed: 01/06/2023]
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Gsell M, Fankl A, Klug L, Mascher G, Schmidt C, Hrastnik C, Zellnig G, Daum G. A Yeast Mutant Deleted of GPH1 Bears Defects in Lipid Metabolism. PLoS One 2015; 10:e0136957. [PMID: 26327557 PMCID: PMC4556709 DOI: 10.1371/journal.pone.0136957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
In a previous study we demonstrated up-regulation of the yeast GPH1 gene under conditions of phosphatidylethanolamine (PE) depletion caused by deletion of the mitochondrial (M) phosphatidylserine decarboxylase 1 (PSD1) (Gsell et al., 2013, PLoS One. 8(10):e77380. doi: 10.1371/journal.pone.0077380). Gph1p has originally been identified as a glycogen phosphorylase catalyzing degradation of glycogen to glucose in the stationary growth phase of the yeast. Here we show that deletion of this gene also causes decreased levels of phosphatidylcholine (PC), triacylglycerols and steryl esters. Depletion of the two non-polar lipids in a Δgph1 strain leads to lack of lipid droplets, and decrease of the PC level results in instability of the plasma membrane. In vivo labeling experiments revealed that formation of PC via both pathways of biosynthesis, the cytidine diphosphate (CDP)-choline and the methylation route, is negatively affected by a Δgph1 mutation, although expression of genes involved is not down regulated. Altogether, Gph1p besides its function as a glycogen mobilizing enzyme appears to play a regulatory role in yeast lipid metabolism.
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Affiliation(s)
- Martina Gsell
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Ariane Fankl
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Lisa Klug
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Gerald Mascher
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Claudia Schmidt
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Claudia Hrastnik
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Günther Zellnig
- Institute of Plant Sciences, Karl Franzens University Graz, NaWi Graz, Austria
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
- * E-mail:
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10
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Gsell M, Mascher G, Schuiki I, Ploier B, Hrastnik C, Daum G. Transcriptional response to deletion of the phosphatidylserine decarboxylase Psd1p in the yeast Saccharomyces cerevisiae. PLoS One 2013; 8:e77380. [PMID: 24146988 PMCID: PMC3795641 DOI: 10.1371/journal.pone.0077380] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 09/05/2013] [Indexed: 11/18/2022] Open
Abstract
In the yeast, Saccharomyces cerevisiae, the synthesis of the essential phospholipid phosphatidylethanolamine (PE) is accomplished by a network of reactions which comprises four different pathways. The enzyme contributing most to PE formation is the mitochondrial phosphatidylserine decarboxylase 1 (Psd1p) which catalyzes conversion of phosphatidylserine (PS) to PE. To study the genome wide effect of an unbalanced cellular and mitochondrial PE level and in particular the contribution of Psd1p to this depletion we performed a DNA microarray analysis with a ∆psd1 deletion mutant. This approach revealed that 54 yeast genes were significantly up-regulated in the absence of PSD1 compared to wild type. Surprisingly, marked down-regulation of genes was not observed. A number of different cellular processes in different subcellular compartments were affected in a ∆psd1 mutant. Deletion mutants bearing defects in all 54 candidate genes, respectively, were analyzed for their growth phenotype and their phospholipid profile. Only three mutants, namely ∆gpm2, ∆gph1 and ∆rsb1, were affected in one of these parameters. The possible link of these mutations to PE deficiency and PSD1 deletion is discussed.
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Affiliation(s)
- Martina Gsell
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Gerald Mascher
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Irmgard Schuiki
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Birgit Ploier
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Claudia Hrastnik
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
- * E-mail:
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Abstract
Glycogen is a branched polymer of glucose that acts as a store of energy in times of nutritional sufficiency for utilization in times of need. Its metabolism has been the subject of extensive investigation and much is known about its regulation by hormones such as insulin, glucagon and adrenaline (epinephrine). There has been debate over the relative importance of allosteric compared with covalent control of the key biosynthetic enzyme, glycogen synthase, as well as the relative importance of glucose entry into cells compared with glycogen synthase regulation in determining glycogen accumulation. Significant new developments in eukaryotic glycogen metabolism over the last decade or so include: (i) three-dimensional structures of the biosynthetic enzymes glycogenin and glycogen synthase, with associated implications for mechanism and control; (ii) analyses of several genetically engineered mice with altered glycogen metabolism that shed light on the mechanism of control; (iii) greater appreciation of the spatial aspects of glycogen metabolism, including more focus on the lysosomal degradation of glycogen; and (iv) glycogen phosphorylation and advances in the study of Lafora disease, which is emerging as a glycogen storage disease.
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Baskaran S, Chikwana VM, Contreras CJ, Davis KD, Wilson WA, DePaoli-Roach AA, Roach PJ, Hurley TD. Multiple glycogen-binding sites in eukaryotic glycogen synthase are required for high catalytic efficiency toward glycogen. J Biol Chem 2011; 286:33999-4006. [PMID: 21835915 DOI: 10.1074/jbc.m111.264531] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycogen synthase is a rate-limiting enzyme in the biosynthesis of glycogen and has an essential role in glucose homeostasis. The three-dimensional structures of yeast glycogen synthase (Gsy2p) complexed with maltooctaose identified four conserved maltodextrin-binding sites distributed across the surface of the enzyme. Site-1 is positioned on the N-terminal domain, site-2 and site-3 are present on the C-terminal domain, and site-4 is located in an interdomain cleft adjacent to the active site. Mutation of these surface sites decreased glycogen binding and catalytic efficiency toward glycogen. Mutations within site-1 and site-2 reduced the V(max)/S(0.5) for glycogen by 40- and 70-fold, respectively. Combined mutation of site-1 and site-2 decreased the V(max)/S(0.5) for glycogen by >3000-fold. Consistent with the in vitro data, glycogen accumulation in glycogen synthase-deficient yeast cells (Δgsy1-gsy2) transformed with the site-1, site-2, combined site-1/site-2, or site-4 mutant form of Gsy2p was decreased by up to 40-fold. In contrast to the glycogen results, the ability to utilize maltooctaose as an in vitro substrate was unaffected in the site-2 mutant, moderately affected in the site-1 mutant, and almost completely abolished in the site-4 mutant. These data show that the ability to utilize maltooctaose as a substrate can be independent of the ability to utilize glycogen. Our data support the hypothesis that site-1 and site-2 provide a "toehold mechanism," keeping glycogen synthase tightly associated with the glycogen particle, whereas site-4 is more closely associated with positioning of the nonreducing end during catalysis.
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Affiliation(s)
- Sulochanadevi Baskaran
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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Díaz A, Martínez-Pons C, Fita I, Ferrer JC, Guinovart JJ. Processivity and subcellular localization of glycogen synthase depend on a non-catalytic high affinity glycogen-binding site. J Biol Chem 2011; 286:18505-14. [PMID: 21464127 DOI: 10.1074/jbc.m111.236109] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Glycogen synthase, a central enzyme in glucose metabolism, catalyzes the successive addition of α-1,4-linked glucose residues to the non-reducing end of a growing glycogen molecule. A non-catalytic glycogen-binding site, identified by x-ray crystallography on the surface of the glycogen synthase from the archaeon Pyrococcus abyssi, has been found to be functionally conserved in the eukaryotic enzymes. The disruption of this binding site in both the archaeal and the human muscle glycogen synthases has a large impact when glycogen is the acceptor substrate. Instead, the catalytic efficiency remains essentially unchanged when small oligosaccharides are used as substrates. Mutants of the human muscle enzyme with reduced affinity for glycogen also show an altered intracellular distribution and a marked decrease in their capacity to drive glycogen accumulation in vivo. The presence of a high affinity glycogen-binding site away from the active center explains not only the long-recognized strong binding of glycogen synthase to glycogen but also the processivity and the intracellular localization of the enzyme. These observations demonstrate that the glycogen-binding site is a critical regulatory element responsible for the in vivo catalytic efficiency of GS.
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Affiliation(s)
- Adelaida Díaz
- Institute for Research in Biomedicine, Universitat de Barcelona, Barcelona, Spain
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14
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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