United States Patent (19) 11 Patent Number: 5,695,752 Rosen Et Al

Total Page:16

File Type:pdf, Size:1020Kb

United States Patent (19) 11 Patent Number: 5,695,752 Rosen Et Al US00569.5752AIII United States Patent (19) 11 Patent Number: 5,695,752 Rosen et al. 45 Date of Patent: Dec. 9, 1997 (54) TREATING INFLAMMATION WIA THE Stoolman et al., “Phosphomannosyl Receptors May Partici ADMINISTRATION OF SPECIFIC pate in the Adhesion Interaction between Lymphocytes and SULFATASE ENZYMES AND/OR SULFATION High Endothelial Venules". J. Cell Biol, 99:1535-1540 INHIBITOR (1984). Willenborg et al., "Phosphosugars are potent inhibitors of 75) Inventors: Steven D. Rosen; Stefan Hemmerich, central nervous system inflammation'. Faseb. J., both of San Francisco, Calif.; Yasuyuki 3:1968-1971 (1989). Imai, Tokyo, Japan Willenborg et al., "Inhibition of Allergic Encephalomyeltis in Rats by Treatment With Sulfated Polysaccharides". J. 73) Assignee: The Regents of the University of Immunol., 140:3401-3405 (1988). California, Oakland, Calif. Brandley, et al., "Cell-Surface Carbohydrates in Cell Rec ognition and Response." J. Leuk. Biol, (1986) 40:97-111. 21 Appi. No.: 496,857 Sharon, et al., "Lectins as Cell Recognition Molecules.” Science, (1989). 246:227-234. 22 Filed: Jun. 30, 1995 Dodd, et al., "Lactoseries Carbohydrates Specify Subsets of Related U.S. Application Data Dorsal Root Ganglion Neurons Projecting to the Superficial Dorsal Horn of Rat Spinal Cord." J. Neurosci, (1985) 63 Continuation of Ser. No. 24,947, Mar 16, 1994, aban 5(12):3278-3294. doned, which is a continuation-in-part of Ser. No. 943,817, Regan, et al., "Selective Expression of Endogenous Lac Sep. 11, 1992, abandoned, and Ser. No. 155,947, Nov. 19, tose-binding Lectins and Lactoseries Glycoconjugates in 1993, abandoned. Subsets of Rat Sensory Neurons.” Proc. Natl. Acad. Sci. (51) Int. Cl. .......................... A61K 38/47; A61K 38/46; USA, (1986) 83:2248-2252. A61K38/43; C12N 9/24 Constantine-Paton, et al., "A Cell Surface Molecule Dis 52 U.S. C. .................... 424/94.61; 424/94.6; 424/94.1; tributed in a Dorsoventral Gradient in the Perinatal Rat 435/196; 435/200 Retina,” Nature, (1986) 324:459–462. 58) Field of Search ................................ 424/94.61, 94.6, Tiemeyer, et al., "Ganglioside-specific Binding Protein on 424/94.1; 435/196, 200 Rat Brain Membranes," J. Bio. Chem, (1989) 264(3):1671-1681. 56) References Cited Bevilacqua, et al., “Identification of an Inducible Endothe lial-Leukocyte Adhesion Molecule." Proc. Natl. Acad. Sci. U.S. PATENT DOCUMENTS USA, (1987) 84:9238-9242. 4,163,783 8/1979 Klein et al. ............................ 424,245 Fukuda, et al., "Structure of a Novel Sialylated Fucosyl 4,370,325 1/1983 Packman ................................. 424.245 Lacto N-nor-hexaosylceramide Isolated from Chronic 4,849,513 7/1989 Smith et al. 536/27 Myelogenous Leukemia Cells,” J. Biol. Chem, (1986) 5,013,724 S/1991 Petitou et al. 514/54 261(5):2376-2383. 5,143,172 9/1992 Brandley et al. ........................ 424/1.1 (List continued on next page.) FOREIGN PATENT DOCUMENTS Primary Examiner-Leon B. Lankford, Jr. WO 92/O2527 2/1992 WIPO : Assistant Examiner-Francisco C. Prats WO92/O2527 2/1992 WTPO Attorney, Agent, or Firm-Karl Bozicevic; Bret Field; OTHER PUBLICATIONS Bozicevic & Reed 57 ABSTRACT Roberton et al. Biochem J. 293:683-689 (1993). Tomatsu et al, Biochem. Biophys. Res. Comm. Compositions are administered to a patient (preferably by 181(2):677-683 (1991). injection and locally) to treat a variety of conditions includ Robertson et al., Biochem. Biophys. Res. Comm. 157(1): ing inflammation associated with trauma and with certain aspects of diseases such as rheumatoid arthritis, psoriasis, 218-224 (1988). insulin-dependent diabetes, cutaneous lymphomas, duode Glabe et al., "Preparation and Properties of Fluorescent nal ulcer, chronic proctitis, lymphocytic thyroidiris, hemor Polysaccharides", Anal. Biochem, 130:287-294 (1983). phagic shock, reperfusion injury during transplantation and Kishimoto et al., "Identification of a human peripheral multiple sclerosis. The compositions are pharmaceutically lymph node homing receptor: A rapidly down-regulated acceptable injectable formulations which include an active adhesion molecule', Proc. Natl. Acad. Sci. USA, component in a pharmaceutically acceptable carrier. The 87:2244-2248 (1990). active component is a chlorate or selenate which inhibits the Lasky, L.A., “Lectin Cell Adhesion Molecules natural biochemical sulfation process and/or a sulfatase (LEC-CAMs): A New Family of Cell Adhesion Proteins enzyme which removes a sulfate from a specific position of Involved With Inflammation". J. Cell Biochem, 45:139-146 a saccharide molecule which makes up a part of a natural (1991). ligand for L-selectin. Removal of the sulfate from the ligand Rosen et al., "L-Selectin: A Lectin-Like Leukocyte Adhe hinders the ability of the ligand to bind to its natural receptor sion Protein", Trends in Glycoscience and Glycotechnology, (i.e. L-selectin) and thereby hinders a biochemical chain of 4:1-13 (1992). events which results in inflammation. Springer, T., “Adhesion Receptors of the Immune System", Nature, 346:425-434 (1990). 6 Claims, 2 Drawing Sheets 5,695,752 Page 2 OTHER PUBLICATIONS Yednock, et al., "Receptors Involved in Lymphocyte Hom ing: Relationship Between a Carbohydrate-binding Recep Magnani, et al., "A Monoclonal Antibody-defined Antigen tor and the MEL-14 Antigen.” J. Cell Biol, (1987) Associated with Gastrointestinal Cancer is a Ganglioside 104:725-731. Containing Sialylated Lacto-N-fucopentaose II." J. Biol. Bevilacqua, et al., "Selectins: A Family of Adhesion Recep Chem, (1982) 257(23):14365-14369. tors." Cell, (1991) 67:233. Hakomori, et al., "Human Cancer-Associated Gangliosides Lasky, et al., “An Endothelial Ligand for L-Selectin Is A Defined by a Monoclonal Antibody (DB9) Directed to Sia Novel Mucin-like Molecule.” Cell, (1992) 69:927-938. losylo2-6 Galactosyl Residue: A Preliminary Note." Bio Rosen, et al., "Involvement of Sialic Acid on Endothelial chem, and Biophys. Res. Conn., (1983) 113(3):791-798. Cells in Organ-Specific Lymphocyte Recirculation." Sci Fukushi, et al., "Localization and Alteration of Mono-, Dl-, ence, (1985) 228:1005-1007. and Trifucosyl oil-3 Type 2 Chain Structures During Imai, et al., "Further Characterization of the Interaction Human Embryogenesis and in Human Cancer," J. Ep. Between L-selectin and its Endothelial Ligands." Glycobi Med., (1984) 159:506-520. ology, (1992) 204):373-381. Geng, et al., "Rapid Neutrophil Adhesion to Activated Siegelman, et al., "Mouse Lymph Node Homing Receptor Endothelium Mediated by GMP-140," Nature, (1990) cDNA Clone Encodes a Glycoprotein Revealing Tandem 343:757-760. Interaction Domains." Science, (1989). 243:1165-1172. Johnston, et al., “Cloning of GMP-140, a Granule Mem Tedder, et al., "Isolation and Chromosomal Localization of brane Protein of Platelets and Endothelium: Sequence Simi cDNAs Encoding a Noval Human Lymphocyte Cell Surface larity to Proteins Involved in Cell Adhesion and Inflamma Molecule. LAM-1." J. Ep. Med., (1989) 170:123-133. tion.” Cell, (1989) 56:1033-1044. Camerini, et al., "Leu-8/TQ1 is the human equivalent of the Geoffroy, et al..."Demonstration that a Lectin-like Receptor Mel-14 lymph node homing receptor,” Nature, (1989) (gp90') Directly Mediates Adhesion of Lymphocytes to 342:78-82. High Endothelial Venules of Lymph Nodes." J. Cell Biol, Stoolman, et al., "Possible Role for Cell-surface Carbohy (1989) 109:2463-2469. drate-binding Molecules in Lymphocyte Recirculation." J. Lasky, et al., "Cloning of a Lymphocyte Homing Receptor Cell Biol, (1983) 96:722-729. Reveals a Lectin Domain." Cell, (1989) 56:1045-1055. Berg, et al., "The Human Peripheral Lymph Node Vascular Bevilacqua, et al., "Endothelial Leukocyte Adhesion Mol Addressin is a Ligand for LECAM-1, the Peripheral Lymph ecule 1: An Inducible Receptor for Neutrophils Related to Node Homing Receptor." J. Cell Biol, (1991) Complement Regulatory Proteins and Lectins." Science, 114(2):343-349. (1989) 243:1160-1165. Streeter, et al., “Immunohistologic and Functional Charac Watson, et al., "Neutrophil Influx into an Inflammatory Site terization of a Vascular Addressin Involved in Lymphocyte Inhibited by a Soluble Homing Receptor-IgG Chimaera.” Homing into Peripheral Lymph Nodes." J. Cell Biol, (1988) Nature, (1991) 349:164-167. 107:1853-1862. Spertini, et al., "Regulation of Leukocyte Migration by Rapraeger, et al., “Requirement of Heparan Sulfate for Activation of the Leukocyte Adhesion Molecule-1 bFGF-Mediated Fibroblast Growth and Myoblast Differen (LAM-1) Selectin.” Nature, (1991) 349:691-694. tiation," Science, (1991) 252: 1705-1708. Imai, et al., "Direct Demonstration of the Lectin Activity of Watson, et al., "A Homing Receptor-IgG Chimera as a gp90', a Lymphocyte Homing Receptor." J. Cell Biol, Probe for Adhesive Ligands of Lymph Node High Endot (1990) 111:1225-1232. helial Venules,” J. Cell Biol, (1990) 110:2221-2229. Imai, et al., “Identification of a Carbohydrate-based Endot Fiete, et al., “A Hepatic Reticuloendothelial Cell Receptor helial Ligand for a Lymphocyte Homing Receptor.” J. Cell Specific for SO4GalNAcB1.4GlcNAc,B12Mano. That Biol, (1991) 113(5):1213-1221. Mediates Rapid Clearance of Lutropin," Cell, (1991) Lerouge, et al., "Symbiotic Host-specificity of Rhizobium 67:1103-1110. meliloti is Determined by a Sulphated and Acylated Glu Roche, et al., “Molecular Basis of Symbiotic Host Speci cosamine Oligosaccharide Signal.” Nature, (1990) ficity in Rhizobium meliloti: nodH and nodPQ Genes Encode 344:781-784. the Sulfation of Lipo-Oligosaccharide Signals." Cell, Fiete, et al., "A Hepatic Reticuloendothelial Cell
Recommended publications
  • Identification and Characterisation of Mucin Abnormalities in the Ganglionic Bowel in Hirschsprung’S Disease
    IDENTIFICATION AND CHARACTERISATION OF MUCIN ABNORMALITIES IN THE GANGLIONIC BOWEL IN HIRSCHSPRUNG’S DISEASE By Ruth Marian Speare Submitted for MD (Res) 1 Abstract Hirschsprung’s disease (HD) is a congenital abnormality of unknown origin, characterised by a lack of ganglion cells in the distal colon which results in functional colonic obstruction. The major cause of morbidity and mortality in these children results from an inflammatory condition called enterocolitis. Mucins are large glycoproteins produced by intestinal cells which are a vital part of the colonic defensive barrier to infection. Previous work has found that this barrier is deficient in children with HD in the aganglionic colon and in the immediately adjacent ganglionic colon and that this is related to the risk of developing enterocolitis. This study aimed to further investigate the mucin defensive barrier in a greater region of the ganglionic colon in HD, to establish the extent of any mucin deficiencies and whether these were confined to a limited region close to the aganglionic colon. Mucosal biopsies were collected at intervals along the colon at the time of corrective surgery or colostomy closure in the controls. Organ culture with radioactive mucin precursors was performed and the mucin produced was purified and analysed, results quantified by DNA content in the sample. Lectin binding studies were also carried out. Patients were found to produce lower levels of new mucins most distally, but much higher levels five centimetres proximal when compared to controls. The rest of the colon studied also showed changes in mucin production, with a lack of production of gel-forming mucins and sulphated secreted mucins in Hirschsprung’s disease higher up the colon.
    [Show full text]
  • Mucin Glycoproteins Are Ubiquitous in Mucous Secretions on Cell Surfaces and in Body fluids
    Chapter 9 – O-GalNAc Glycans - Essentials of Glycobiology 2nd edition Intestinal mucosal barrier function in health and disease. Turner, JR Nature Rev. Immunology 9: 799 (2009) From Mucins to Mucus Thornton DJ and Sheehan JK, Proc Am Thorac Soc., 1:54 (2004) Mucin structure, aggregation, physiological functions and biomedical applications Bansil R. and Turner BS Curr Opin in Colloid & Interface Sci, 11:164 (2006) Mucins in the mucosal barrier to infection Linden et al, Nature Immunology 1: 183 (2008) The cancer glycocalyx mechanically primes integrin-mediated growth and survival. Paszek et al, Nature 511: 319 (2014) Chapter 9 – O-GalNAc Glycans Essentials of Glycobiology 2nd edition 4/14/2016 O-GalNAc Glycans - Essentials of Glycobiology - NCBI Bookshelf NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health. Varki A, Cummings RD, Esko JD, et al., editors. Essentials of Glycobiology. 2nd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2009. Chapter 9O-GalNAc Glycans Inka Brockhausen, Harry Schachter, and Pamela Stanley. Correction O-glycosylation is a common covalent modification of serine and threonine residues of mammalian glycoproteins. This chapter describes the structures, biosynthesis, and functions of glycoproteins that are often termed mucins. In mucins, O-glycans are covalently α-linked via an N-acetylgalactosamine (GalNAc) moiety to the -OH of serine or threonine by an O-glycosidic bond, and the structures are named mucin O-glycans or O-GalNAc glycans. The focus of this chapter is on mucins and mucin-like glycoproteins that are heavily O-glycosylated, although glycoproteins that carry only one or a few O- GalNAc glycans are also briefly discussed.
    [Show full text]
  • Two Glycosulfatases from the Liver of a Marine Gastropod , Charonia Lampas
    J. Biochem., 79, 27-34 (1976) Two Glycosulfatases from the Liver of a Marine Gastropod , Charonia lampas Partial Purification and Properties1 Hiroshi HATANAKA, Yoko OGAWA , and Fujio EGAMI Mitsubishi-Kasei Institute of Life Sciences , Minamiooya, Machida-shi, Tokyo 194 Received for publication , July 9, 1975 Two glycosulfatases [EC 3.1 .6.3], I and ‡U, were purified 31 .3- and 33.9-fold respectively, from a crude extract of the liver of Charonia lampas . The purification was carried out by the following chromatographic procedures ; phosphocellulose , S ephadex G-150, Concanavalin A-Sepharose and isoelectric focussing . The enzyme preparations obtained were practically free from arylsulfatase [EC 3.1.6.1] contami nation. Both glycosulfatases are probably glycoproteins differing in their carbohydrate moieties. The molecular weights of glycosulfatase I and H were estimated to be about 112,000 and 79 ,000, respectively. They had the same optimum pH of 5.5, and the same Km value of 25.0mM for glucose 6-sulfate . As a result of recent investigations on sul yet been fully investigated. Glycosulfatase was fatase reactions, the physiological significance found first in molluscs by Soda and co-workers of arylsulfatase [EC 3. 1. 6. 1] is gradually being (10) and later in microorganisms, but its oc- elucidated. The hydrolysis of naturally oc currence in higher animals is doubtful (11). curring sugar-sulfate derivatives by arylsul In the present investigation, we studied fatase has been reported in the cases of sulfo the partial purification and some properties of galactolipids (1-5), UDP - N- acetylgalacto two glycosulfatases from the liver of a marine samine 4-sulfate (6, 7), and ascorbate 2-sulfate gastropod, Charonia lampas.
    [Show full text]
  • Molecular and Biochemical Characterisation of Siap As a Sialic Acid Binding Protein Component of a TRAP Transporter for Sialic Acid
    Molecular and biochemical characterisation of SiaP as a sialic acid binding protein component of a TRAP transporter for sialic acid Adam Paul Hopkins A thesis submitted for the degree of Doctor of Philosophy University of York Department of Biology July 2010 Abstract Sialic acid utilisation plays an important role in the growth and persistence of the obligate human mucosal pathogen Haemophilus influenzae, which causes respiratory tract infections, septicaemia and meningitis. Like many other bacteria, H. influenzae can use host-derived sialic acids as carbon, nitrogen and energy sources, but also as a terminal modification on the LPS to better evade the human immune system. H. influenzae takes up exogenous sialic acid via a tripartite ATP-independent periplasmic (TRAP) transporter, SiaPQM. This possesses an extracytoplasmic substrate binding protein (SBP), SiaP, which binds the substrate in the periplasm and delivers it to the specific membrane permease, SiaQM. SiaP contains two globular domains, which close around the substrate upon binding. Here, the mechanism of sialic acid binding by SiaP is investigated using site-directed mutagenesis of residues in the ligand binding site and analogues of sialic acid. These, and several mutations on the surface of SiaP, were investigated for their effect on transport by SiaPQM in vitro, using SiaQM reconstituted into proteoliposomes, and in vivo, using expression of siaPQM in an E. coli strain lacking its native sialic acid transporter, NanT. It is demonstrated that stabilisation of the carboxylate group of sialic acid by the totally conserved Arginine-147 is important for high-affinity ligand binding, but is not essential for transport. Mutation of Aparagine-150 to Aspartate abolishes the function of the transporter without affecting ligand binding, suggesting the existence of a critical interaction between the components of the transporter.
    [Show full text]
  • A Single Bacterial Sulfatase Is Required for Metabolism of Colonic Mucin O-Glycans and Intestinal Colonization by a Symbiotic Hu
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.20.392076; this version posted November 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 2 A single bacterial sulfatase is required for metabolism of colonic mucin O-glycans 3 and intestinal colonization by a symbiotic human gut bacterium 4 5 *1,2Ana S. Luis, 2Chunsheng Jin, 1Gabriel Vasconcelos Pereira, 1Robert W. P. Glowacki, 6 1Sadie Gugel, 1Shaleni Singh, 3Dominic P. Byrne, 1Nicholas Pudlo, 3James A London, 7 4Arnaud Baslé, 5Mark Reihill, 5Stefan Oscarson, 3Patrick A. Eyers, 6Mirjam, Czjzek, 8 6Gurvan Michel, 6Tristan Barbeyron, 3Edwin A Yates, 2Gunnar C. Hansson, 2Niclas G. 9 Karlsson, *,3Alan Cartmell, *1Eric C. Martens 10 11 12 13 1Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 14 48109, USA 15 2Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, 16 University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden 17 3Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and 18 Integrative Biology, University of Liverpool, Liverpool L69 3BX, United Kingdom 19 4Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon 20 Tyne, United Kingdom 21 5Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 22 4, Ireland. 23 6Sorbonne Université, Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine 24 Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France.
    [Show full text]
  • 12) United States Patent (10
    US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S.
    [Show full text]
  • Biomarker Identification in Human Lung Adenocarcinoma
    Research Collection Doctoral Thesis Activity-based proteomics biomarker identification in human lung adenocarcinoma Author(s): Wiedl, Thomas Publication Date: 2011 Permanent Link: https://doi.org/10.3929/ethz-a-006698733 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Diss. ETH Nr. 19704 Activity-based proteomics: biomarker identification in human lung adenocarcinoma A dissertation submitted to the ETH Zurich for the degree of Doctor of Sciences (Dr. sc. ETH Zurich) presented by Thomas Wiedl Dipl. Ing., Vienna University of Technology, Austria Born March 30, 1981 Citizen of Austria accepted on the recommendation of Prof. Dr. Rudolf Aebersold (examiner) Prof. Dr. Walter Weder (co-examiner) Prof. Dr. Holger Moch (co-examiner) Prof. Dr. Stephan Sieber (co-examiner) 2011 Table of contents SUMMARY 6 ZUSAMMENFASSUNG 8 ACKNOWLEDGEMENTS 10 ABBREVIATIONS 12 1. INTRODUCTION 14 1.1 LUNG CANCER : CLASSIFICATION , EPIDEMIOLOGY AND PROGNOSIS 14 1.2 MOLECULAR EVOLUTION OF LUNG CANCER 16 1.3 LUNG CANCER AND THE BIOMARKER CONCEPT : STATUS QUO 18 1.4 MASS SPECTROMETRY (MS) BASED PROTEOMICS 20 1.5 ACTIVITY -BASED PROTEOMICS : A NOVEL STRATEGY FOR BIOMARKER DISCOVERY 23 1.6 THE SERINE HYDROLASE SUPERFAMILY 26 1.7 LUNG CANCER IN THE FUTURE 29 2. MATERIAL AND METHODS 30 2.1 SAMPLE COLLECTION 30 2.2 CELL CULTURE AND LYSIS 31 2.3 WESTERN BLOT 31 2.4 ACTIVITY -BASED PROBE 32 2.5 PROTEOME PREPARATION FOR LC-MS/MS ANALYSIS 33 2.6 LC-MS/MS ANALYSIS 35 2.7 DATABASE SEARCH AND LABEL -FREE QUANTIFICATION 36 2.8 STATISTICAL ANALYSIS 37 3.
    [Show full text]
  • Detection of Bacterial Sulfatase Activity Through Liquid- and Solid-Phase Colony-Based Assays
    Yoon et al. AMB Expr (2017) 7:150 DOI 10.1186/s13568-017-0449-3 ORIGINAL ARTICLE Open Access Detection of bacterial sulfatase activity through liquid‑ and solid‑phase colony‑based assays Hey Young Yoon1†, Hyung Jun Kim2†, Soojin Jang2 and Jong‑In Hong1* Abstract Bacterial arylsulfatases are crucial to biosynthesis in many microorganisms, as bacteria often utilize aryl sulfates as a source of sulfur. The bacterial sulfatases are associated with pathogenesis and are applied in many areas such as industry and agriculture. We developed an activity-based probe 1 for detection of bacterial sulfatase activity through liquid- and solid-phase colony-based assays. Probe 1 is hydrolyzed by sulfatase to generate fuorescent N-methyl isoindole, which is polymerized to form colored precipitates. These fuorescent and colorimetric properties of probe 1 induced upon treatment of sulfatases were successfully utilized for liquid-phase sulfatase activity assays for colonies and lysates of Klebsiella aerogenes, Mycobacterium avium and Mycobacterium smegmatis. In addition, probe 1 allowed solid-phase colony-based assays of K. aerogenes through the formation of insoluble colored precipitates, thus ena‑ bling accurate staining of target colonies under heterogeneous conditions. Keywords: Bacterial sulfatase, Activity-based probe, N-methyl isoindole, Colony-based assay, Liquid-phase assay, Solid-phase assay Introduction 2015). Teir activities are strongly infuenced by bacterial Sulfur is a chemical element essential to all organisms, as growth environmental conditions and thus their meas- it is required for the biosynthesis of cysteine and methio- urements can be used for soil quality assessment (Garcia- nine; it is also involved in many redox reactions that take Sanchez et al.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur Et Al
    US 2012026.6329A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur et al. (43) Pub. Date: Oct. 18, 2012 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/10 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/24 (2006.01) CI2N 9/02 (2006.01) (75) Inventors: Eric J. Mathur, Carlsbad, CA CI2N 9/06 (2006.01) (US); Cathy Chang, San Marcos, CI2P 2L/02 (2006.01) CA (US) CI2O I/04 (2006.01) CI2N 9/96 (2006.01) (73) Assignee: BP Corporation North America CI2N 5/82 (2006.01) Inc., Houston, TX (US) CI2N 15/53 (2006.01) CI2N IS/54 (2006.01) CI2N 15/57 2006.O1 (22) Filed: Feb. 20, 2012 CI2N IS/60 308: Related U.S. Application Data EN f :08: (62) Division of application No. 1 1/817,403, filed on May AOIH 5/00 (2006.01) 7, 2008, now Pat. No. 8,119,385, filed as application AOIH 5/10 (2006.01) No. PCT/US2006/007642 on Mar. 3, 2006. C07K I4/00 (2006.01) CI2N IS/II (2006.01) (60) Provisional application No. 60/658,984, filed on Mar. AOIH I/06 (2006.01) 4, 2005. CI2N 15/63 (2006.01) Publication Classification (52) U.S. Cl. ................... 800/293; 435/320.1; 435/252.3: 435/325; 435/254.11: 435/254.2:435/348; (51) Int. Cl. 435/419; 435/195; 435/196; 435/198: 435/233; CI2N 15/52 (2006.01) 435/201:435/232; 435/208; 435/227; 435/193; CI2N 15/85 (2006.01) 435/200; 435/189: 435/191: 435/69.1; 435/34; CI2N 5/86 (2006.01) 435/188:536/23.2; 435/468; 800/298; 800/320; CI2N 15/867 (2006.01) 800/317.2: 800/317.4: 800/320.3: 800/306; CI2N 5/864 (2006.01) 800/312 800/320.2: 800/317.3; 800/322; CI2N 5/8 (2006.01) 800/320.1; 530/350, 536/23.1: 800/278; 800/294 CI2N I/2 (2006.01) CI2N 5/10 (2006.01) (57) ABSTRACT CI2N L/15 (2006.01) CI2N I/19 (2006.01) The invention provides polypeptides, including enzymes, CI2N 9/14 (2006.01) structural proteins and binding proteins, polynucleotides CI2N 9/16 (2006.01) encoding these polypeptides, and methods of making and CI2N 9/20 (2006.01) using these polynucleotides and polypeptides.
    [Show full text]
  • All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
    All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA
    [Show full text]
  • Bacterial Glycosulphatases and Sulphomucin Degradation
    PEDIATRIC GASTROENTEROLOGY Bacterial glycosulphatases and sulphomucin degradation Anthony M Roberton BSc(Hons) DPhil, Damian P Wright MSc AM Roberton, DP Wright. Bacterial glycosulphatases and sul- Glycosulfatases bactériennes et dégradation de phomucin degradation. Can J Gastroenterol 1997;11(4):361- 366. The presence of a high bacterial population in a region of the la sulfomucine gastrointestinal tract is usually associated with the secretion of sul- RÉSUMÉ : La présence d’une forte population bactérienne dans une ré- phomucins into the mucus gel covering that region. The term ‘su- gion du tractus digestif est habituellement associée à la sécrétion de sul- lphomucin’ is a histochemical description of the staining fomucines dans le gel muqueux qui tapisse cette région. Le terme properties of mucin. At present this term can only be qualitatively sulfomucine est une description histochimique des propriétés colorantes de related to the percentage of sulphate in the mucin molecule, la mucine. À l’heure actuelle, ce terme ne peut être que qualitativement as- which makes the term difficult to use in a biochemical and func- socié au pourcentage de sulfate présent dans la molécule de mucine, ce qui tional sense. Sulphomucins are thought to carry out the normal rend son emploi difficile dans un sens biochimique et fonctionnel. Les sul- functions attributed to mucins; in addition, heavy sulphation fomucines accompliraient des fonctions normalement attribuées aux mu- rate-limits the degradation of mucins by bacterial mucin- cines; de plus, de forts taux de sulfatation limitent la dégradation des degrading glycosidases. A number of mucin-specific glycosul- mucines par les glycosidases responsables de la dégradation de la mucine phatases have been reported in bacteria, although only two such bactérienne.
    [Show full text]
  • Universal Protein Families and the Functional Content of the Last Universal Common Ancestor
    J Mol Evol (1999) 49:413–423 © Springer-Verlag New York Inc. 1999 Universal Protein Families and the Functional Content of the Last Universal Common Ancestor Nikos Kyrpides,1,2 Ross Overbeek,2 Christos Ouzounis3 1 Department of Microbiology, University of Illinois at Urbana–Champaign, 407 South Goodwin Avenue, Urbana IL 61801, USA 2 Mathematics and Computer Science Division, Argonne National Laboratory, 9700 South Case Avenue, Argonne IL 60439, USA 3 Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK Abstract. The phylogenetic distribution of Metha- ties of a complete set of archaeal proteins with the other nococcus jannaschii proteins can provide, for the first two domains, Bacteria and Eukarya. This universal set of time, an estimate of the genome content of the last com- protein families present in all domains can then be used mon ancestor of the three domains of life. Relying on as an estimate for the genome content of the Last Uni- annotation and comparison with reference to the species versal Common Ancestor (Woese 1982; Woese and Fox distribution of sequence similarities results in 324 pro- 1977). Evidently, factors such as gene loss, horizontal teins forming the universal family set. This set is very transfer across domains and species peculiarities make well characterized and relatively small and nonredun- this task difficult, especially when only interspecies com- dant, containing 301 biochemical functions, of which parisons are used (Becerra et al. 1997). Previous such 246 are unique. This universal function set contains approaches have ignored the above problems (Mush- mostly genes coding for energy metabolism or informa- egian and Koonin 1996), resulting in descriptions that tion processing.
    [Show full text]