Articles Catalytic Cycling in Β-Phosphoglucomutase: a Kinetic
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Annual Report DDUV 2009
Research at the de Duve Institute and Brussels Branch of the Ludwig Institute for Cancer Research August 2009 de Duve Institute Introduction 5 Miikka Vikkula 12 Frédéric Lemaigre 20 Annabelle Decottignies and Charles de Smet 25 Emile Vanschaftingen 31 Françoise Bontemps 37 Jean-François Collet 42 Guido Bommer 47 Mark Rider 50 Fred Opperdoes 56 Pierre Courtoy 62 Etienne Marbaix 69 Jean-Baptiste Demoulin 75 Jean-Paul Coutelier 80 Thomas Michiels 84 Pierre Coulie 89 LICR Introduction 95 Benoît Van den Eynde 98 Pierre van der Bruggen 106 Nicolas Van Baren 114 Jean-Christophe Renauld 119 Stefan Constantinescu 125 The de Duve Institute 5 THE DE DUVE INSTITUTE: AN INTERNATIONAL BIOMEDICAL RESEARCH INSTITUTE In 1974, when Christian de Duve founded the Institute of Cellular Pathology (ICP), now rena- med the de Duve Institute, he was acutely aware of the constrast between the enormous progress in biological sciences that had occurred in the 20 preceding years and the modesty of the medical advances that had followed. He therefore crea- ted a research institution based on the principle that basic research in biology would be pursued by the investigators with complete freedom, but that special attention would be paid to the exploi- tation of basic advances for medical progress. It was therefore highly appropriate for the Institute to be located on the campus of the Faculty of Emile Van Schaftingen Medicine of the University of Louvain (UCL). This campus is located in Brussels. The Univer- sity hospital (Clinique St Luc) is located within walking distance of the Institute. The main commitment of the members of the de Duve Institute is research. -
Diagnosis, Treatment and Follow Up
DOI: 10.1002/jimd.12024 REVIEW International clinical guidelines for the management of phosphomannomutase 2-congenital disorders of glycosylation: Diagnosis, treatment and follow up Ruqaiah Altassan1,2 | Romain Péanne3,4 | Jaak Jaeken3 | Rita Barone5 | Muad Bidet6 | Delphine Borgel7 | Sandra Brasil8,9 | David Cassiman10 | Anna Cechova11 | David Coman12,13 | Javier Corral14 | Joana Correia15 | María Eugenia de la Morena-Barrio16 | Pascale de Lonlay17 | Vanessa Dos Reis8 | Carlos R Ferreira18,19 | Agata Fiumara5 | Rita Francisco8,9,20 | Hudson Freeze21 | Simone Funke22 | Thatjana Gardeitchik23 | Matthijs Gert4,24 | Muriel Girad25,26 | Marisa Giros27 | Stephanie Grünewald28 | Trinidad Hernández-Caselles29 | Tomas Honzik11 | Marlen Hutter30 | Donna Krasnewich18 | Christina Lam31,32 | Joy Lee33 | Dirk Lefeber23 | Dorinda Marques-da-Silva9,20 | Antonio F Martinez34 | Hossein Moravej35 | Katrin Õunap36,37 | Carlota Pascoal8,9 | Tiffany Pascreau38 | Marc Patterson39,40,41 | Dulce Quelhas14,42 | Kimiyo Raymond43 | Peymaneh Sarkhail44 | Manuel Schiff45 | Małgorzata Seroczynska29 | Mercedes Serrano46 | Nathalie Seta47 | Jolanta Sykut-Cegielska48 | Christian Thiel30 | Federic Tort27 | Mari-Anne Vals49 | Paula Videira20 | Peter Witters50,51 | Renate Zeevaert52 | Eva Morava53,54 1Department of Medical Genetic, Montréal Children's Hospital, Montréal, Québec, Canada 2Department of Medical Genetic, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia 3Department of Human Genetics, KU Leuven, Leuven, Belgium 4LIA GLYCOLAB4CDG (International -
Supplementary Table S1. Table 1. List of Bacterial Strains Used in This Study Suppl
Supplementary Material Supplementary Tables: Supplementary Table S1. Table 1. List of bacterial strains used in this study Supplementary Table S2. List of plasmids used in this study Supplementary Table 3. List of primers used for mutagenesis of P. intermedia Supplementary Table 4. List of primers used for qRT-PCR analysis in P. intermedia Supplementary Table 5. List of the most highly upregulated genes in P. intermedia OxyR mutant Supplementary Table 6. List of the most highly downregulated genes in P. intermedia OxyR mutant Supplementary Table 7. List of the most highly upregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Table 8. List of the most highly downregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Figures: Supplementary Figure 1. Comparison of the genomic loci encoding OxyR in Prevotella species. Supplementary Figure 2. Distribution of SOD and glutathione peroxidase genes within the genus Prevotella. Supplementary Table S1. Bacterial strains Strain Description Source or reference P. intermedia V3147 Wild type OMA14 isolated from the (1) periodontal pocket of a Japanese patient with periodontitis V3203 OMA14 PIOMA14_I_0073(oxyR)::ermF This study E. coli XL-1 Blue Host strain for cloning Stratagene S17-1 RP-4-2-Tc::Mu aph::Tn7 recA, Smr (2) 1 Supplementary Table S2. Plasmids Plasmid Relevant property Source or reference pUC118 Takara pBSSK pNDR-Dual Clonetech pTCB Apr Tcr, E. coli-Bacteroides shuttle vector (3) plasmid pKD954 Contains the Porpyromonas gulae catalase (4) -
Glycogenesis
Glycogenesis Glycogen is the storage form of glucose in animals and humans which is analogous to the starch in plants. Glycogen is synthesized and stored mainly in the liver and the muscles. Structurally, glycogen is very similar to amylopectin with alpha acetal linkages, however, it has even more branching and more glucose units are present than in amylopectin. Various samples of glycogen have been measured at 1,700-600,000 units of glucose. The structure of glycogen consists of long polymer chains of glucose units connected by an alpha acetal linkage. All of the monomer units are alpha-D-glucose, and all the alpha acetal links connect C # 1 of one glucose to C # 4 of the next glucose. The branches are formed by linking C # 1 to a C # 6 through acetal linkages. In glycogen, the branches occur at intervals of 8-10 glucose units (in amylopectin the branches are separated by 12-20 glucose units). Carbon # 1 is called the anomeric carbon and is the center of an acetal functional group. The Alpha position is defined as the ether oxygen being on the opposite side of the ring as the C # 6. In the chair structure this results in a downward projection. Plants make starch and cellulose through the photosynthesis processes. Animals and human in turn eat plant materials and products. Digestion is a process of hydrolysis where the starch is broken ultimately into the various monosaccharides. A major product is of course glucose which can be used immediately for metabolism to make energy. The glucose that is not used immediately is converted in the liver and muscles into glycogen for storage by the process of glycogenesis. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Transcriptomic and Proteomic Profiling Provides Insight Into
BASIC RESEARCH www.jasn.org Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy † † ‡ Peidi Liu,* Emelie Lassén,* Viji Nair, Celine C. Berthier, Miyuki Suguro, Carina Sihlbom,§ † | † Matthias Kretzler, Christer Betsholtz, ¶ Börje Haraldsson,* Wenjun Ju, Kerstin Ebefors,* and Jenny Nyström* *Department of Physiology, Institute of Neuroscience and Physiology, §Proteomics Core Facility at University of Gothenburg, University of Gothenburg, Gothenburg, Sweden; †Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan; ‡Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan; |Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; and ¶Integrated Cardio Metabolic Centre, Karolinska Institutet Novum, Huddinge, Sweden ABSTRACT IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN (n=19) and controls (n=22). Using curated glomerular cell type–specific genes from the published literature, we found differential expression of a much higher percentage of mesangial cell–positive standard genes than podocyte-positive standard genes in IgAN. Principal coordinate analysis of expression data revealed clear separation of patient and control samples on the basis of mesangial but not podocyte cell–positive standard genes. -
Letters to Nature
letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997). -
Expression of a Phosphoglucomutase Gene in Rainbow Trout (Polymorphism/Developmental Rate/Glycolysis/Salmo Gairdneri) FRED W
Proc. Natt Acad. Sci. USA Vol. 80, pp. 1397-1400, March 1983 Genetics Adaptive significance of differences in the tissue-specific expression of a phosphoglucomutase gene in rainbow trout (polymorphism/developmental rate/glycolysis/Salmo gairdneri) FRED W. ALLENDORF, KATHY L. KNUDSEN, AND ROBB F. LEARY Department of Zoology,, University of Montana, Missoula, Montana 59812 Communicated by G. Ledyard Stebbins, November 17, 1982 ABSTRACT We have investigated the phenotypic effects of fold increase in the expression of a phosphoglucomutase (PGM; a mutant allele that results in the expression of a phosphogluco- a-D-glucose-1,6-bisphosphate:a-D-glucose-l-phosphate phos- mutase locus (Pgml) in the liver of rainbow trout. Embryos with photransferase EC 2.7.5. 1) locus, Pgml, in liver tissue (14, 15). liver Pgml expression hatch earlier than embryos without liver The results of inheritance experiments are consistent with a sin- Pgml expression. These differences apparently result from in- gle regulatory gene, Pgml-t, with additive inheritance being re- creased flux through glycolysis in embryos with liver PGM1 ac- sponsible for the differences in the expression of this locus (15). tivity while they are dependent on the yolk for energy. Fish with We report here that the presence or absence of PGM1 in the liver PGM1 activity are also more developmentally buffered, as liver rise to indicated by less fluctuating asymmetry of five bilateral meristic gives important differences in several phenotypic traits. The more rapidly developing individuals begin exogenous characteristics of adaptive significance (developmental rate, de- feeding earlier and achieve a size advantage that is maintained velopmental stability, body size, and age at first maturity). -
The Reaction Mechanism of Phosphomannomutase in Plants
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector FEBS 18031 FEBS Letters 401 (1997) 35-37 The reaction mechanism of phosphomannomutase in plants Christine Oesterhelt, Claus Schnarrenberger, Wolfgang Gross* Institut für Pflanzenphysiologie und Mikrobiologie, Freie Universität Berlin, Königin-Luise-Str. 12-16a, D-14195 Berlin, Germany Received 11 November 1996 the presence of an excess of GIC-I.6-P2, purified PMM from G. sul- Abstract The enzyme phosphomannomutase catalyzes the phuraria, pig brain, and yeast was incubated with 1 mM GIC-I.6-P2 interconversion of mannose-1-phosphate (Man-l-P) and man- and 0.1 mM Man-l-P for 3 h at room temperature. The reaction nose-6-phosphate (Man-6-P). In mammalian cells the enzyme products were separated by TLC at pH 10 as described [8]. The has to be activated by transfer of a phosphate group from a corresponding regions for Man-l-P, Man-6-P, and Glc-6-P were sugar-1.6-P2 (Guha, S.K. and Rose, Z.B. (1985) Arch. Biochem. scraped off, the sugar phosphates eluted, and identified enzymatically. Biophys. 243, 168). In contrast, in the red alga Galdieria The concentration of Glc-6-P was determined by the addition of Glc- sulphuraria the co-substrate (Man-1.6-P2 or GIC-I.6-P2) is 6-P dehydrogenase and NADP. For Man-6-P determination PGI and PMI were included and for Man-l-P purified PMM from G. sulphu- converted to the corresponding sugar monophosphate while the raria was added. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
Lecture 8 - Glycogen Metabolism
Lecture 8 - Glycogen Metabolism Chem 454: Regulatory Mechanisms in Biochemistry University of Wisconsin-Eau Claire Introduction Glycogen Text A storage form of glucose 2 Introduction Glycogen is stored primarily in the liver and Text skeletal muscles. Liver - used for maintaining blood glucose levels Muscles - used to meet energy needs of the muscles 3 Introduction Glycogen Text degradation occurs in three steps 4 Introduction Glycogen Text synthesis uses activated precursor UDP–glucose 5 Introduction Regulation of glycogen metabolism is Text complex. Allosteric regulation to meet the needs of the cell Hormonal regulation to meet the needs of the organsim 6 1. Glycogen Breakdown Requires three enzymes and produces Text glucose 6–phosphate Glycogen Phosphorylase Debranching Enzyme Phosphoglucomutase In the liver, an additional enzyme produces free glucose Glucose 6–phosphatase 7 1.1 Phosphorylase Cleavage uses orthophosphate in Text phosphorolysis reactions glycogen + Pi glucose 1-phosphate + glycogen n residues n-1 residues 8 1.2 Debranching Enzyme Two enzymes Text activities are needed to deal with the α–1,6 branch points 9 1.3 Phosphoglucomutase Mechanism is like that of phosphoglycerate Text mutase 10 1.4 Glucose 6-phosphatase Enzyme is found primarily in the liver and is Text used to release glucose into the bloodstream glucose 6-phosphate + H2O glucose + Pi 11 1.5 Mechanism for Phosphorolysis Text 12 1.5 Mechanism for Phosphorolysis Pyridoxyl phosphate Text coenzyme 13 1.5 Mechanism for Phosphorolysis Text 14 2. Regulation of Phosphorylase Phosphorylase is regulated by several Text allosteric effectors that signal the energy state of the cell It is also regulated by reversible phosphorylation in response to the hormones insulin, epinephrine, and glucagon 15 2.1 Muscle Phosphorylase Text 16 2.1 Muscle Phosphorylase Text 17 2.1 Muscle Phosphorylase Text 18 2.2 Liver Phosphorylase Text 19 2.3 Phosphorylase Kinase Text 20 3. -
TABLE S3 Clusters of Gene Ontology Groups and Their Associated Genes
TABLE S3 Clusters of gene ontology groups and their associated genes found altered with Colchicine resistance (KB-8-5 vs KB-3-1) Annereau J-P, Szakacs G, Tucker CJ, Arciello A, Cardarelli C, Collins J, Grissom S, Zeeberg B, Reinhold W, Weinstein J, Pommier Y, Paules RS, and Gottesman MM (2004) Analysis of ABC transporter expression in drug-selected cell lines by a microarray dedicated to multidrug resistance. Mol Pharmacol doi:10.1124/mol.104.005009. a Gene Ontology subgroups and references HUGO HUGO gene description Antigen presentation GO:0030333 antigen_processing HLA-E + major histocompatibility complex, class i, e GO:0030106 MHC_class_I_receptor_activity HLA-C + major histocompatibility complex, class i, c GO:0019885 antigen_processing,_endogenous_antigen_via_MHC_class_I HLA-B + major histocompatibility complex, class i, b GO:0019883 antigen_presentation,_endogenous_antigen HLA-A + major histocompatibility complex, class i, a GO:0019882 antigen_presentation B2M + beta-2-microglobulin Metabolism of carbonhydrate ALDOA - fructose-bisphosphate aldolase a GO:0019320 tricarboxylic_acid_cycle ATP5J - atp synthase, h+ transporting, mitochondrial GO:0006007 monosaccharide_metabolism COX6C - cytochrome c oxidase, subunit vic GO:0046365 monosaccharide_catabolism DLD - dihydrolipoamide dehydrogenase, phe3 GO:0046164 main_pathways_of_carbohydrate_metabolism G6PD - glucose-6-phosphate dehydrogenase GO:0019320 hexose_metabolism GAPD - glyceraldehyde-3-phosphate dehydrogenase GO:0019318 hexose_catabolism HDLBP - high density lipoprotein binding