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Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_003722335Cyc: Caulobacter flavus RHGG3 Cellular Overview Connections between pathways are omitted for legibility.

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ATP-Citrate Lyase Has an Essential Role in Cytosolic Acetyl-Coa Production in Arabidopsis Beth Leann Fatland Iowa State University
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2002 ATP-citrate lyase has an essential role in cytosolic acetyl-CoA production in Arabidopsis Beth LeAnn Fatland Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Molecular Biology Commons, and the Plant Sciences Commons Recommended Citation Fatland, Beth LeAnn, "ATP-citrate lyase has an essential role in cytosolic acetyl-CoA production in Arabidopsis " (2002). Retrospective Theses and Dissertations. 1218. https://lib.dr.iastate.edu/rtd/1218 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. ATP-citrate lyase has an essential role in cytosolic acetyl-CoA production in Arabidopsis by Beth LeAnn Fatland A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Plant Physiology Program of Study Committee: Eve Syrkin Wurtele (Major Professor) James Colbert Harry Homer Basil Nikolau Martin Spalding Iowa State University Ames, Iowa 2002 UMI Number: 3158393 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted.
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Generated by SRI International Pathway Tools Version 25.0, Authors S
An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility.
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Mannosidases Are the Putative Catabolic Enzymes Which
THE CHARACTERIZATION OF A NOVEL HUMAN CORE-SPECIFIC LYSOSOMAL α1-6MANNOSIDASE INVOLVED IN N-GLYCAN CATABOLISM by CHAEHO PARK (Under the Direction of Kelley W. Moremen) ABSTRACT In humans and rodents lysosomal catabolism of Man3GlcNAc2 core N-glycan structures results from the concerted actions of exoglycosidases including the broad specificity lysosomal α- mannosidase (LysMan), a core-specific α1-6mannosidase, and β-mannosidase, as well as the core chitobiose cleavage by an di-N-acetylchitobiase. In ungulates and carnivora, both the chitobiase and the α1-6mannosidase enzyme activities are absent suggesting a co-regulation of the two enzymes. We describe here the cloning, expression, purification and characterization of the human core-specific α1-6mannosidase with similarity to members of the glycosylhydrolase family 38. The recombinant enzyme had a pH optimum of 4.0, was potently inhibited by swainsonine and 1,4-dideoxy1,4-imino-D-mannitol, and was stimulated by Co+2. NMR-based time course substrate specificity studies comparing the α1-6mannosidase with human LysMan revealed that the former enzyme selectively cleaved the α1-6mannose residue from Man3GlcNAc, but not Man3GlcNAc2 or other larger high mannose structures, indicating the requirement for chitobiase action prior to α1-6mannosidase cleavage. In contrast, LysMan cleaved all of the α-linked mannose residues from Man9-5GlcNAc2, Man3GlcNAc2, or Man3GlcNAc structures except the core α1-6mannose residue. Transcripts encoding the α1-6mannosidase were ubiquitously expressed in human tissues and expressed sequence tag searches in various mammalian species demonstrated a similar distribution in species-specific expression as the chitobiase. No expressed sequence tags were identified for bovine α1-6mannosidase despite the identification of two homologs in the bovine genome.
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Liver Glucose Metabolism in Humans
Biosci. Rep. (2016) / 36 / art:e00416 / doi 10.1042/BSR20160385 Liver glucose metabolism in humans Mar´ıa M. Adeva-Andany*1, Noemi Perez-Felpete*,´ Carlos Fernandez-Fern´ andez*,´ Cristobal´ Donapetry-Garc´ıa* and Cristina Pazos-Garc´ıa* *Nephrology Division, Hospital General Juan Cardona, c/ Pardo Bazan´ s/n, 15406 Ferrol, Spain Synopsis Information about normal hepatic glucose metabolism may help to understand pathogenic mechanisms underlying obesity and diabetes mellitus. In addition, liver glucose metabolism is involved in glycosylation reactions and con- nected with fatty acid metabolism. The liver receives dietary carbohydrates directly from the intestine via the portal vein. Glucokinase phosphorylates glucose to glucose 6-phosphate inside the hepatocyte, ensuring that an adequate ﬂow of glucose enters the cell to be metabolized. Glucose 6-phosphate may proceed to several metabolic path- ways. During the post-prandial period, most glucose 6-phosphate is used to synthesize glycogen via the formation of glucose 1-phosphate and UDP–glucose. Minor amounts of UDP–glucose are used to form UDP–glucuronate and UDP– galactose, which are donors of monosaccharide units used in glycosylation. A second pathway of glucose 6-phosphate metabolism is the formation of fructose 6-phosphate, which may either start the hexosamine pathway to produce UDP-N-acetylglucosamine or follow the glycolytic pathway to generate pyruvate and then acetyl-CoA. Acetyl-CoA may enter the tricarboxylic acid (TCA) cycle to be oxidized or may be exported to the cytosol to synthesize fatty acids, when excess glucose is present within the hepatocyte. Finally, glucose 6-phosphate may produce NADPH and ribose 5-phosphate through the pentose phosphate pathway.
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Two Pectate Lyases from Caldicellulosiruptor Bescii with the Same CALG Domain Had
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.16.910000; this version posted January 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Two pectate lyases from Caldicellulosiruptor bescii with the same CALG domain had 2 distinct properties on plant biomass degradation 3 Hamed I. Hamoudaa,b,c, Nasir Alia, Hang Sua,b, Jie Fenga, Ming Lua,†and Fu-Li Li a,† 4 a Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuel, 5 Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 6 Qingdao 266101, China 7 b University of Chinese Academy of Sciences, Beijing 100039, China. 8 c Egyptian Petroleum Research Institute, Nasr City 11727, Cairo, Egypt. 9 †Corresponding authors: Dr. Ming Lu (E-mail: [email protected]) and Dr. Fu-Li Li 10 (E-mail: [email protected]), Qingdao Institute of Bioenergy and Bioprocess Technology, 11 Chinese Academy of Sciences, Qingdao 266101, China 12 13 Keywords: Caldicellulosiruptor, Pectin, Pectate lyase, Polysaccharide lyase, Concanavalin 14 A-like lectin/glucanase (CALG) 15 16 17 18 19 20 21 22 23 24 25 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.16.910000; this version posted January 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 26 Abstract 27 Pectin deconstruction is the initial step in breaking the recalcitrance of plant biomass by using 28 selected microorganisms that carry pectinolytic enzymes.
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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
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Open Matthew R Moreau Ph.D. Dissertation Finalfinal.Pdf
The Pennsylvania State University The Graduate School Department of Veterinary and Biomedical Sciences Pathobiology Program PATHOGENOMICS AND SOURCE DYNAMICS OF SALMONELLA ENTERICA SEROVAR ENTERITIDIS A Dissertation in Pathobiology by Matthew Raymond Moreau 2015 Matthew R. Moreau Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 The Dissertation of Matthew R. Moreau was reviewed and approved* by the following: Subhashinie Kariyawasam Associate Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Bhushan M. Jayarao Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Mary J. Kennett Professor, Veterinary and Biomedical Sciences Vijay Kumar Assistant Professor, Department of Nutritional Sciences Anthony Schmitt Associate Professor, Veterinary and Biomedical Sciences Head of the Pathobiology Graduate Program *Signatures are on file in the Graduate School iii ABSTRACT Salmonella enterica serovar Enteritidis (SE) is one of the most frequent common causes of morbidity and mortality in humans due to consumption of contaminated eggs and egg products. The association between egg contamination and foodborne outbreaks of SE suggests egg derived SE might be more adept to cause human illness than SE from other sources. Therefore, there is a need to understand the molecular mechanisms underlying the ability of egg- derived SE to colonize the chicken intestinal and reproductive tracts and cause disease in the human host. To this end, the present study was carried out in three objectives. The first objective was to sequence two egg-derived SE isolates belonging to the PFGE type JEGX01.0004 to identify the genes that might be involved in SE colonization and/or pathogenesis.
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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.
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Molecular Cloning and Knockdown of Galactocerebrosidase in Zebrafish
Biochimica et Biophysica Acta 1842 (2014) 665–675 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbadis Molecular cloning and knockdown of galactocerebrosidase in zebrafish: New insights into the pathogenesis of Krabbe's disease Daniela Zizioli a,1, Michela Guarienti a,1,ChiaraTobiab, Giuseppina Gariano b, Giuseppe Borsani c, Roberto Bresciani a,RobertoRoncab, Edoardo Giacopuzzi c, Augusto Preti a, Germano Gaudenzi d, Mirella Belleri b, Emanuela Di Salle b, Gemma Fabrias e, Josefina Casas e,DomenicoRibattif,g, Eugenio Monti a,MarcoPrestab,⁎ a Unit of Biotechnology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy b Unit of Oncology and Experimental Immunology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy c Unit of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy d Department of Biology, University of Milan, Milan, Italy e Research Unit on Bioactive Molecules (RUBAM), Department of Biomedicinal Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Council for Scientific Research (CSIC), Barcelona, Spain f Department of Basic Biomedical Sciences, Unit of Human Anatomy and Histology, University of Bari, Bari, Italy g National Cancer Institute, Giovanni Paolo II, Bari, Italy article info abstract Article history: The lysosomal hydrolase galactocerebrosidase (GALC) catalyzes the removal of galactose from galactosylceramide Received 2 September 2013 and from other sphingolipids. GALC deficiency is responsible for globoid cell leukodystrophy (GLD), or Krabbe's Received in revised form 17 December 2013 disease, an early lethal inherited neurodegenerative disorder characterized by the accumulation of the neurotoxic Accepted 15 January 2014 metabolite psychosine in the central nervous system (CNS).
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Glycosphingolipids Are Modulators of Disease Pathogenesis in Amyotrophic Lateral Sclerosis
Glycosphingolipids are modulators of disease pathogenesis in amyotrophic lateral sclerosis James C. Dodgea,1, Christopher M. Treleavena, Joshua Pachecoa, Samantha Coopera,ChannaBaoa, Marissa Abrahama, Mandy Cromwella, S. Pablo Sardia, Wei-Lien Chuanga, Richard L. Sidmanb,1,2,SengH.Chenga, and Lamya S. Shihabuddina aRare Diseases Science, Genzyme, a Sanofi Company, Framingham, MA 01701; and bBeth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 Contributed by Richard L. Sidman, May 7, 2015 (sent for review January 12, 2015; reviewed by David V. Schaffer) Recent genetic evidence suggests that aberrant glycosphingolipid mediates the hydrolysis of Cer, are linked to forms of spinal metabolism plays an important role in several neuromuscular muscular atrophy that are not caused by the more frequent mu- diseases including hereditary spastic paraplegia, hereditary sen- tations in the survival motor neuron 1 gene (non-5q SMA) (15). sory neuropathy type 1, and non-5q spinal muscular atrophy. Here, Moreover, hereditary spastic paraplegia (HSP), a disease with cor- we investigated whether altered glycosphingolipid metabolism is ticospinal tract and in some cases, spinal cord MN degeneration, a modulator of disease course in amyotrophic lateral sclerosis (ALS). is attributed to mutations in GM2 synthase (16) and the non- Levels of ceramide, glucosylceramide, galactocerebroside, lactosyl- lysosomal glucosylceramidase, GBA2 (17). Last, patients with adult- ceramide, globotriaosylceramide, and the gangliosides GM3 and onset Tay-Sachs disease (GM2 gangliosidosis), a disease triggered GM1 were significantly elevated in spinal cords of ALS patients. by a deficiency in hexosaminidase (HEX), a lysosomal enzyme Moreover, enzyme activities (glucocerebrosidase-1, glucocerebrosi- that hydrolyzes GM2 to GM3, have been reported in some in- dase-2, hexosaminidase, galactosylceramidase, α-galactosidase, and stances to display a disease phenotype that closely mimics ALS β-galactosidase) mediating glycosphingolipid hydrolysis were also (18–20).
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A Single Mutation Affects Both N-Acetylglucosaminyltransferase
Proc. Natl. Acad. Sci. USA Vol. 89, pp. 2267-2271, March 1992 Biochemistry A single mutation affects both N-acetylglucosaminyltransferase and glucuronosyltransferase activities in a Chinese hamster ovary cell mutant defective in heparan sulfate biosynthesis (glycosaminoglycans/proteoglycans/glycosyltransferases/replica plating) KERSTIN LIDHOLT*, JULIE L. WEINKEt, CHERYL S. KISERt, FULGENTIUS N. LUGEMWAt, KAREN J. BAMEtt, SELA CHEIFETZ§, JOAN MASSAGUO§, ULF LINDAHL*¶1, AND JEFFREY D. ESKOt II tDepartment of Biochemistry, Schools of Medicine and Dentistry, University of Alabama, Birmingham, AL 35294; *Depaltment of Veterinary Medical Chemistry, The Biomedical Center, Swedish University of Agricultural Sciences, S-751 23, Uppsala, Sweden; and §Department of Cell Biology and Genetics, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021 Communicated by Marilyn G. Farquhar, December 10, 1991 ABSTRACT Mutants of Chinese hamster ovary cells have bovine serum. A resistant mutant was isolated and then been found that no longer produce heparan sulfate. Charac- treated with mutagen (7), and a ouabain-resistant clone was terization of one of the mutants, pgsD-677, showed that it lacks selected in growth medium containing 1 mM ouabain. The both N-acetylglucosaminyl- and glucuronosyltransferase, en- introduction of these markers did not alter the proteoglycan zymes required for the polymerization of heparan sulfate composition of the cells. chains. pgsD-677 also accumulates 3- to 4-fold more chon- Cell hybrids were generated by co-plating 2 x 105 cells of droitin sulfate than the wild type. Cell hybrids derived from pgsD-677 and OT-1 in individual wells of a 24-well plate. pgsD-677 and wild type regained both transferase activities and After overnight incubation, the mixed monolayers were the capacity to synthesize heparan sulfate.
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The Genome of an Industrial Workhorse
NEWS AND VIEWS The genome of an industrial workhorse Dan Cullen Sequencing of the filamentous fungus Aspergillus niger offers new opportunities for the production of specialty chemicals and enzymes. Few microbes compare with the filamentous fungus Aspergillus niger in its ability to pro Environment CAT (2) H O H O + O duce prodigious amounts of useful chemicals 2 2 2 2 and enzymes. This fungus is the principal GOX (3) GLN (1) source of citric acid for food, beverages and D-glucono Glucose Gluconate Oxalate pharmaceuticals1 and of several important 1,5-lactone Citrate http://www.nature.com/naturebiotechnology http://www.nature.com/naturebiotechnology commercial enzymes, including glucoamy lase, which is widely used for the conversion of starch to food syrups and to fermentative Oxalate + acetate PEP feedstocks for ethanol production. Although OAH most of these fermentation processes are well cMDH (3) established, the underlying genetics are still cPYC (1) cACO (2) cIDH (1) poorly understood. In this issue, Pel et al.2 Pyruvate OAA MAL Citrate Isocitrate 2-ketoglutarate report the genome sequence of A. niger strain Cytosol CBS 513.88. The availability of this sequence OAT (1) CMC (2) mPYC (1) should provide invaluable aid toward improv Pyruvate OAA MAL Citrate Isocitrate 2-ketoglutarate ing the production of chemicals and enzymes PDH Nature Publishing Group Group Nature Publishing 7 in this organism. mMDH (1) mACO (2) mIDH (3) Pel et al. sequenced tiled bacterial artificial CS (3) 200 Acetyl-CoA TCA cycle © chromosomes representing the entire A. niger genome to produce a high-quality assembly of Mitochondrion 19 supercontigs with a combined length of 33.9 Mb.
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